monai-weekly 1.6.dev2622__tar.gz → 1.6.dev2623__tar.gz

{monai_weekly-1.6.dev2622/monai_weekly.egg-info → monai_weekly-1.6.dev2623}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: monai-weekly
-Version: 1.6.dev2622
+Version: 1.6.dev2623
 Summary: AI Toolkit for Healthcare Imaging
 Home-page: https://project-monai.github.io/
 Author: MONAI Consortium
@@ -56,7 +56,7 @@ Requires-Dist: imagecodecs; (platform_system == "Linux" or platform_system == "D
 Requires-Dist: pandas; extra == "all"
 Requires-Dist: einops; extra == "all"
 Requires-Dist: transformers>=4.53.0; extra == "all"
-Requires-Dist: mlflow>=2.12.2; extra == "all"
+Requires-Dist: mlflow<3.13,>=2.12.2; extra == "all"
 Requires-Dist: clearml>=1.10.0rc0; extra == "all"
 Requires-Dist: matplotlib>=3.6.3; extra == "all"
 Requires-Dist: tensorboardX; extra == "all"
@@ -120,7 +120,7 @@ Requires-Dist: einops; extra == "einops"
 Provides-Extra: transformers
 Requires-Dist: transformers<4.41.0,>=4.36.0; python_version <= "3.10" and extra == "transformers"
 Provides-Extra: mlflow
-Requires-Dist: mlflow>=2.12.2; extra == "mlflow"
+Requires-Dist: mlflow<3.13,>=2.12.2; extra == "mlflow"
 Provides-Extra: matplotlib
 Requires-Dist: matplotlib>=3.6.3; extra == "matplotlib"
 Provides-Extra: clearml

{monai_weekly-1.6.dev2622 → monai_weekly-1.6.dev2623}/monai/__init__.py

@@ -136,4 +136,4 @@ except Exception:
 
     if MONAIEnvVars.debug():
         raise
-__commit_id__ = "dc0f59c9fdbd7f631d42dbea66147ae5b4135dc2"
+__commit_id__ = "2a7d0cf05c82dde97fd4b26f5fe9b9ab4e2100fe"

{monai_weekly-1.6.dev2622 → monai_weekly-1.6.dev2623}/monai/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2026-05-31T03:11:19+0000",
+ "date": "2026-06-07T03:11:31+0000",
  "dirty": false,
  "error": null,
- "full-revisionid": "77568cc7d532e00c6c994fd80f39c1a20e9c6ba3",
- "version": "1.6.dev2622"
+ "full-revisionid": "ae09234cb82c33f61353886bfc0baa1418abac55",
+ "version": "1.6.dev2623"
 }
 '''  # END VERSION_JSON
 

{monai_weekly-1.6.dev2622 → monai_weekly-1.6.dev2623}/monai/apps/nnunet/nnunetv2_runner.py

@@ -14,6 +14,7 @@ from __future__ import annotations
 
 import glob
 import os
+import re
 import shlex
 import subprocess
 from typing import Any
@@ -34,6 +35,8 @@ logger = monai.apps.utils.get_logger(__name__)
 
 __all__ = ["nnUNetV2Runner"]
 
+DATASET_ID_FORMAT = r"Dataset[0-9]{3}|[0-9]+"  # regex format for a valid nnUnet dataset name
+
 
 class nnUNetV2Runner:  # noqa: N801
     """
@@ -195,6 +198,13 @@ class nnUNetV2Runner:  # noqa: N801
 
         # dataset_name_or_id has to be a string
         self.dataset_name_or_id = str(self.input_info.pop("dataset_name_or_id", 1))
+        self.dataset_name: str | None = None
+
+        # ensure the dataset name is a single identifier/number, this prevents code injection when composing commands
+        if re.fullmatch(DATASET_ID_FORMAT, self.dataset_name_or_id) is None:
+            raise ValueError(
+                f"Value for dataset_name_or_id `{self.dataset_name_or_id}` not a valid dataset name or ID."
+            )
 
         try:
             from nnunetv2.utilities.dataset_name_id_conversion import maybe_convert_to_dataset_name
@@ -239,7 +249,7 @@ class nnUNetV2Runner:  # noqa: N801
 
             from nnunetv2.utilities.dataset_name_id_conversion import maybe_convert_to_dataset_name
 
-            self.dataset_name = maybe_convert_to_dataset_name(int(self.dataset_name_or_id))
+            self.dataset_name = maybe_convert_to_dataset_name(self.dataset_name_or_id)
 
             datalist_json = ConfigParser.load_config_file(self.input_info.pop("datalist"))
 
@@ -548,7 +558,7 @@ class nnUNetV2Runner:  # noqa: N801
         Raises:
             ValueError: If gpu_id is an empty tuple or list.
         """
-        env = os.environ.copy()
+        env: dict[str, str] = os.environ.copy()
         device_setting: str = "0"
         num_gpus = 1
         if isinstance(gpu_id, str):
@@ -574,22 +584,25 @@ class nnUNetV2Runner:  # noqa: N801
 
         cmd = [
             "nnUNetv2_train",
-            f"{self.dataset_name_or_id}",
-            f"{config}",
-            f"{fold}",
+            self.dataset_name_or_id,
+            config,
+            fold,
             "-tr",
-            f"{self.trainer_class_name}",
+            self.trainer_class_name,
             "-num_gpus",
-            f"{num_gpus}",
+            num_gpus,
         ]
+
         if self.export_validation_probabilities:
             cmd.append("--npz")
+
         for _key, _value in kwargs.items():
-            if _key == "p" or _key == "pretrained_weights":
-                cmd.extend([f"-{_key}", f"{_value}"])
-            else:
-                cmd.extend([f"--{_key}", f"{_value}"])
-        return cmd, env
+            prefix = "-" if _key in {"p", "pretrained_weights"} else "--"
+            cmd += [f"{prefix}{_key}", str(_value)]
+
+        cmd_str: list[str] = [str(c) for c in cmd]
+
+        return cmd_str, env
 
     def train(
         self,
@@ -641,7 +654,14 @@ class nnUNetV2Runner:  # noqa: N801
                 None (all available GPUs).
             kwargs: this optional parameter allows you to specify additional arguments defined in the
                 ``train_single_model`` method.
+
+        Raises:
+            ValueError: self.dataset_name must have a value, ie. when using an existing dataset or after creating one.
         """
+
+        if self.dataset_name is None:
+            raise ValueError(f"A valid dataset name must be given in {self.dataset_name=}.")
+
         # unpack compressed files
         folder_names = []
         for root, _, files in os.walk(os.path.join(self.nnunet_preprocessed, self.dataset_name)):
@@ -696,7 +716,14 @@ class nnUNetV2Runner:  # noqa: N801
                 None (all available GPUs).
             kwargs: this optional parameter allows you to specify additional arguments defined in the
                 ``train_single_model`` method.
+
+        Raises:
+            ValueError: self.dataset_name must have a value, ie. when using an existing dataset or after creating one.
         """
+
+        if self.dataset_name is None:
+            raise ValueError(f"A valid dataset name must be given in {self.dataset_name=}.")
+
         all_cmds = self.train_parallel_cmd(configs=configs, gpu_id_for_all=gpu_id_for_all, **kwargs)
         for s, cmds in enumerate(all_cmds):
             for gpu_id, gpu_cmd in cmds.items():
@@ -908,7 +935,14 @@ class nnUNetV2Runner:  # noqa: N801
             run_postprocessing: whether to conduct post-processing
             kwargs: this optional parameter allows you to specify additional arguments defined in the
                 ``predict`` method.
+
+        Raises:
+            ValueError: self.dataset_name must have a value, ie. when using an existing dataset or after creating one.
         """
+
+        if self.dataset_name is None:
+            raise ValueError(f"A valid dataset name must be given in {self.dataset_name=}.")
+
         from nnunetv2.ensembling.ensemble import ensemble_folders
         from nnunetv2.postprocessing.remove_connected_components import apply_postprocessing_to_folder
         from nnunetv2.utilities.file_path_utilities import get_output_folder

{monai_weekly-1.6.dev2622 → monai_weekly-1.6.dev2623}/monai/data/image_reader.py

@@ -1231,17 +1231,26 @@ class NumpyReader(ImageReader):
         npz_keys: if loading npz file, only load the specified keys, if None, load all the items.
             stack the loaded items together to construct a new first dimension.
         channel_dim: if not None, explicitly specify the channel dim, otherwise, treat the array as no channel.
+        allow_pickle: if True, allows loading pickled contents from NPY/NPZ files. Note that the default value of False
+            prevents the risk of remote code execution, set this to True only for loading known trusted data. If this
+            argument is False and pickled data is loaded, a ValueError will be raised.
         kwargs: additional args for `numpy.load` API except `allow_pickle`. more details about available args:
             https://numpy.org/doc/stable/reference/generated/numpy.load.html
-
     """
 
-    def __init__(self, npz_keys: KeysCollection | None = None, channel_dim: str | int | None = None, **kwargs):
+    def __init__(
+        self,
+        npz_keys: KeysCollection | None = None,
+        channel_dim: str | int | None = None,
+        allow_pickle: bool = False,
+        **kwargs,
+    ):
         super().__init__()
         if npz_keys is not None:
             npz_keys = ensure_tuple(npz_keys)
         self.npz_keys = npz_keys
         self.channel_dim = float("nan") if channel_dim == "no_channel" else channel_dim
+        self.allow_pickle = allow_pickle
         self.kwargs = kwargs
 
     def verify_suffix(self, filename: Sequence[PathLike] | PathLike) -> bool:
@@ -1267,6 +1276,8 @@ class NumpyReader(ImageReader):
                 More details about available args:
                 https://numpy.org/doc/stable/reference/generated/numpy.load.html
 
+        Raises:
+            ValueError: when `self.allow_pickle` is False but loaded data contains pickled objects.
         """
         img_: list[Nifti1Image] = []
 
@@ -1274,7 +1285,16 @@ class NumpyReader(ImageReader):
         kwargs_ = self.kwargs.copy()
         kwargs_.update(kwargs)
         for name in filenames:
-            img = np.load(name, allow_pickle=True, **kwargs_)
+            try:
+                img = np.load(name, allow_pickle=self.allow_pickle, **kwargs_)
+            except ValueError as e:
+                # if a ValueError is raised, this is likely about pickle loading so raise an exception about this
+                raise ValueError(
+                    "MONAI default value for argument `allow_pickle` of `np.load` changed to `False`, "
+                    "explicitly pass `allow_pickle=True` as a constructor argument to NumpyReader "
+                    "to enable pickle loading."
+                ) from e
+
             if Path(name).name.endswith(".npz"):
                 # load expected items from NPZ file
                 npz_keys = list(img.keys()) if self.npz_keys is None else self.npz_keys

{monai_weekly-1.6.dev2622 → monai_weekly-1.6.dev2623}/monai/losses/image_dissimilarity.py

@@ -233,9 +233,11 @@ class GlobalMutualInformationLoss(_Loss):
         self.kernel_type = look_up_option(kernel_type, ["gaussian", "b-spline"])
         self.num_bins = num_bins
         self.kernel_type = kernel_type
+        self.bin_centers: torch.Tensor | None
+        self.register_buffer("bin_centers", None, persistent=False)
         if self.kernel_type == "gaussian":
             self.preterm = 1 / (2 * sigma**2)
-            self.bin_centers = bin_centers[None, None, ...]
+            self.register_buffer("bin_centers", bin_centers[None, None, ...], persistent=False)
         self.smooth_nr = float(smooth_nr)
         self.smooth_dr = float(smooth_dr)
 
@@ -314,6 +316,8 @@ class GlobalMutualInformationLoss(_Loss):
         """
         img = torch.clamp(img, 0, 1)
         img = img.reshape(img.shape[0], -1, 1)  # (batch, num_sample, 1)
+        if self.bin_centers is None:
+            raise ValueError("bin_centers must be defined for gaussian parzen windowing.")
         weight = torch.exp(
             -self.preterm.to(img) * (img - self.bin_centers.to(img)) ** 2
         )  # (batch, num_sample, num_bin)

{monai_weekly-1.6.dev2622 → monai_weekly-1.6.dev2623}/monai/networks/blocks/crossattention.py

@@ -11,6 +11,8 @@
 
 from __future__ import annotations
 
+from typing import Optional
+
 import torch
 import torch.nn as nn
 
@@ -139,7 +141,7 @@ class CrossAttentionBlock(nn.Module):
         )
         self.input_size = input_size
 
-    def forward(self, x: torch.Tensor, context: torch.Tensor | None = None):
+    def forward(self, x: torch.Tensor, context: Optional[torch.Tensor] = None):  # noqa: UP045
         """
         Args:
             x (torch.Tensor): input tensor. B x (s_dim_1 * ... * s_dim_n) x C

{monai_weekly-1.6.dev2622 → monai_weekly-1.6.dev2623}/monai/networks/blocks/selfattention.py

@@ -11,6 +11,8 @@
 
 from __future__ import annotations
 
+from typing import Optional
+
 import torch
 import torch.nn as nn
 import torch.nn.functional as F
@@ -158,7 +160,7 @@ class SABlock(nn.Module):
         )
         self.input_size = input_size
 
-    def forward(self, x, attn_mask: torch.Tensor | None = None):
+    def forward(self, x, attn_mask: Optional[torch.Tensor] = None):  # noqa: UP045
         """
         Args:
             x (torch.Tensor): input tensor. B x (s_dim_1 * ... * s_dim_n) x C

{monai_weekly-1.6.dev2622 → monai_weekly-1.6.dev2623}/monai/networks/blocks/transformerblock.py

@@ -11,6 +11,8 @@
 
 from __future__ import annotations
 
+from typing import Optional
+
 import torch
 import torch.nn as nn
 
@@ -23,6 +25,11 @@ class TransformerBlock(nn.Module):
     An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale <https://arxiv.org/abs/2010.11929>"
     """
 
+    # Treat ``with_cross_attention`` as a TorchScript constant so the cross-attention branch in
+    # ``forward`` is pruned when it is False. Otherwise scripting tries to compile the
+    # ``self.cross_attn(..., context=context)`` call against ``nn.Identity`` and fails.
+    __constants__ = ["with_cross_attention"]
+
     def __init__(
         self,
         hidden_size: int,
@@ -102,7 +109,10 @@ class TransformerBlock(nn.Module):
             self.cross_attn = nn.Identity()
 
     def forward(
-        self, x: torch.Tensor, context: torch.Tensor | None = None, attn_mask: torch.Tensor | None = None
+        self,
+        x: torch.Tensor,
+        context: Optional[torch.Tensor] = None,  # noqa: UP045
+        attn_mask: Optional[torch.Tensor] = None,  # noqa: UP045
     ) -> torch.Tensor:
         x = x + self.attn(self.norm1(x), attn_mask=attn_mask)
         if self.with_cross_attention:

{monai_weekly-1.6.dev2622 → monai_weekly-1.6.dev2623/monai_weekly.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: monai-weekly
-Version: 1.6.dev2622
+Version: 1.6.dev2623
 Summary: AI Toolkit for Healthcare Imaging
 Home-page: https://project-monai.github.io/
 Author: MONAI Consortium
@@ -56,7 +56,7 @@ Requires-Dist: imagecodecs; (platform_system == "Linux" or platform_system == "D
 Requires-Dist: pandas; extra == "all"
 Requires-Dist: einops; extra == "all"
 Requires-Dist: transformers>=4.53.0; extra == "all"
-Requires-Dist: mlflow>=2.12.2; extra == "all"
+Requires-Dist: mlflow<3.13,>=2.12.2; extra == "all"
 Requires-Dist: clearml>=1.10.0rc0; extra == "all"
 Requires-Dist: matplotlib>=3.6.3; extra == "all"
 Requires-Dist: tensorboardX; extra == "all"
@@ -120,7 +120,7 @@ Requires-Dist: einops; extra == "einops"
 Provides-Extra: transformers
 Requires-Dist: transformers<4.41.0,>=4.36.0; python_version <= "3.10" and extra == "transformers"
 Provides-Extra: mlflow
-Requires-Dist: mlflow>=2.12.2; extra == "mlflow"
+Requires-Dist: mlflow<3.13,>=2.12.2; extra == "mlflow"
 Provides-Extra: matplotlib
 Requires-Dist: matplotlib>=3.6.3; extra == "matplotlib"
 Provides-Extra: clearml

{monai_weekly-1.6.dev2622 → monai_weekly-1.6.dev2623}/monai_weekly.egg-info/requires.txt

@@ -21,7 +21,7 @@ openslide-bin
 pandas
 einops
 transformers>=4.53.0
-mlflow>=2.12.2
+mlflow<3.13,>=2.12.2
 clearml>=1.10.0rc0
 matplotlib>=3.6.3
 tensorboardX
@@ -103,7 +103,7 @@ lpips==0.1.4
 matplotlib>=3.6.3
 
 [mlflow]
-mlflow>=2.12.2
+mlflow<3.13,>=2.12.2
 
 [nibabel]
 nibabel

{monai_weekly-1.6.dev2622 → monai_weekly-1.6.dev2623}/setup.cfg

@@ -68,7 +68,7 @@ all =
 	pandas
 	einops
 	transformers>=4.53.0
-	mlflow>=2.12.2
+	mlflow>=2.12.2,<3.13
 	clearml>=1.10.0rc0
 	matplotlib>=3.6.3
 	tensorboardX
@@ -132,7 +132,7 @@ einops =
 transformers = 
 	transformers>=4.36.0, <4.41.0; python_version <= '3.10'
 mlflow = 
-	mlflow>=2.12.2
+	mlflow>=2.12.2,<3.13
 matplotlib = 
 	matplotlib>=3.6.3
 clearml =