monai-weekly 1.7.dev2627__tar.gz → 1.7.dev2629__tar.gz

{monai_weekly-1.7.dev2627/monai_weekly.egg-info → monai_weekly-1.7.dev2629}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: monai-weekly
-Version: 1.7.dev2627
+Version: 1.7.dev2629
 Summary: AI Toolkit for Healthcare Imaging
 Home-page: https://project-monai.github.io/
 Author: MONAI Consortium
@@ -117,6 +117,8 @@ Provides-Extra: pandas
 Requires-Dist: pandas; extra == "pandas"
 Provides-Extra: einops
 Requires-Dist: einops; extra == "einops"
+Provides-Extra: hyena
+Requires-Dist: nvsubquadratic>=0.1.1; extra == "hyena"
 Provides-Extra: transformers
 Requires-Dist: transformers<4.41.0,>=4.36.0; python_version <= "3.10" and extra == "transformers"
 Provides-Extra: mlflow

{monai_weekly-1.7.dev2627 → monai_weekly-1.7.dev2629}/monai/__init__.py

@@ -136,4 +136,4 @@ except Exception:
 
     if MONAIEnvVars.debug():
         raise
-__commit_id__ = "eb74488c5be06e97d8ee5d6bdec2488ac3903a1c"
+__commit_id__ = "5da247209955bcc29de706d858eeed75f4f08cab"

{monai_weekly-1.7.dev2627 → monai_weekly-1.7.dev2629}/monai/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2026-07-05T03:07:50+0000",
+ "date": "2026-07-19T03:05:24+0000",
  "dirty": false,
  "error": null,
- "full-revisionid": "9c37af81ef49b616038685d338f97726a0266440",
- "version": "1.7.dev2627"
+ "full-revisionid": "52cab21b1eb940ad0c4ea70165f09ec6e7cbaebb",
+ "version": "1.7.dev2629"
 }
 '''  # END VERSION_JSON
 

{monai_weekly-1.7.dev2627 → monai_weekly-1.7.dev2629}/monai/data/image_reader.py

@@ -735,9 +735,22 @@ class PydicomReader(ImageReader):
             metadata: metadata with dict type.
             lps_to_ras: whether to convert the affine matrix from "LPS" to "RAS". Defaults to True.
 
+        Warns:
+            UserWarning: when ImageOrientationPatient (00200037) or ImagePositionPatient
+                (00200032) is missing from metadata. The affine matrix is set to identity,
+                which may be incorrect. Common with multiframe DICOM files.
+
         """
         affine: np.ndarray = np.eye(4)
         if not ("00200037" in metadata and "00200032" in metadata):
+            warnings.warn(
+                "PydicomReader: ImageOrientationPatient (0020,0037) and/or "
+                "ImagePositionPatient (0020,0032) tags are missing, so the affine "
+                "matrix cannot be derived and defaults to the identity. The image "
+                "orientation and spacing may be incorrect (e.g. for multi-frame "
+                "Enhanced DICOM); consider using ITKReader for such files.",
+                stacklevel=2,
+            )
             return affine
         # "00200037" is the tag of `ImageOrientationPatient`
         rx, ry, rz, cx, cy, cz = metadata["00200037"]["Value"]

{monai_weekly-1.7.dev2627 → monai_weekly-1.7.dev2629}/monai/losses/__init__.py

@@ -14,6 +14,7 @@ from __future__ import annotations
 from .adversarial_loss import PatchAdversarialLoss
 from .aucm_loss import AUCMLoss
 from .barlow_twins import BarlowTwinsLoss
+from .boundary_loss import BoundaryLoss
 from .cldice import SoftclDiceLoss, SoftDiceclDiceLoss
 from .contrastive import ContrastiveLoss
 from .deform import BendingEnergyLoss, DiffusionLoss

monai_weekly-1.7.dev2629/monai/losses/boundary_loss.py

@@ -0,0 +1,233 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+import warnings
+from collections.abc import Callable
+
+import torch
+from torch.nn.modules.loss import _Loss
+
+from monai.networks import one_hot
+from monai.transforms.utils import distance_transform_edt
+from monai.utils import LossReduction
+
+__all__ = ["BoundaryLoss"]
+
+
+class BoundaryLoss(_Loss):
+    """
+    Compute the boundary loss for highly unbalanced segmentation.
+
+    The boundary loss is a distance-based loss that operates on the interface between segmentation
+    regions rather than on the regions themselves. This makes it particularly effective for
+    highly imbalanced segmentation tasks (e.g., small lesions, thin structures), where standard
+    Dice or Cross-Entropy losses struggle due to foreground-background imbalance.
+
+    The loss is formulated as a pixel-wise weighted sum of predicted probabilities and a
+    signed distance map derived from the ground truth. The signed distance map is negative
+    inside the foreground region and positive outside, with zero on the boundary.
+
+    The data `input` (BNHW[D] where N is number of classes) is compared with ground truth `target`
+    (BNHW[D]).
+    Note that axis N of `input` is expected to be logits or probabilities for each class, if passing logits as input,
+    must set `sigmoid=True` or `softmax=True`, or specifying `other_act`. And the same axis of `target`
+    can be 1 or N (one-hot format).
+
+    The original paper:
+        Kervadec, H. et al. (2019) Boundary loss for highly unbalanced segmentation. MIDL 2019.
+        https://arxiv.org/abs/1812.07032
+
+    Example:
+        >>> import torch
+        >>> from monai.losses import BoundaryLoss
+        >>> B, C, H, W = 2, 3, 5, 5
+        >>> input = torch.rand(B, C, H, W)
+        >>> target = torch.randint(0, C, size=(B, H, W))
+        >>> bl = BoundaryLoss(softmax=True, to_onehot_y=True)
+        >>> loss = bl(input, target)
+    """
+
+    def __init__(
+        self,
+        include_background: bool = True,
+        to_onehot_y: bool = False,
+        sigmoid: bool = False,
+        softmax: bool = False,
+        other_act: Callable | None = None,
+        reduction: LossReduction | str = LossReduction.MEAN,
+        batch: bool = False,
+    ) -> None:
+        """
+        Args:
+            include_background: if False, channel index 0 (background category) is excluded from the calculation.
+                if the non-background segmentations are small compared to the total image size they can get overwhelmed
+                by the signal from the background so excluding it in such cases helps convergence.
+            to_onehot_y: whether to convert the ``target`` into the one-hot format,
+                using the number of classes inferred from `input` (``input.shape[1]``). Defaults to False.
+            sigmoid: if True, apply a sigmoid function to the prediction.
+            softmax: if True, apply a softmax function to the prediction.
+            other_act: callable function to execute other activation layers, Defaults to ``None``. for example:
+                ``other_act = torch.tanh``.
+            reduction: {``"none"``, ``"mean"``, ``"sum"``}
+                Specifies the reduction to apply to the output. Defaults to ``"mean"``.
+
+                - ``"none"``: no reduction will be applied.
+                - ``"mean"``: the sum of the output will be divided by the number of elements in the output.
+                - ``"sum"``: the output will be summed.
+            batch: whether to compute the distance map and loss over the batch dimension before the dividing.
+                Defaults to False, a boundary loss value is computed independently from each item in the batch
+                before any `reduction`.
+
+        Raises:
+            TypeError: When ``other_act`` is not an ``Optional[Callable]``.
+            ValueError: When more than 1 of [``sigmoid=True``, ``softmax=True``, ``other_act is not None``].
+                Incompatible values.
+        """
+        super().__init__(reduction=LossReduction(reduction).value)
+        if other_act is not None and not callable(other_act):
+            raise TypeError(f"other_act must be None or callable but is {type(other_act).__name__}.")
+        if int(sigmoid) + int(softmax) + int(other_act is not None) > 1:
+            raise ValueError("Incompatible values: more than 1 of [sigmoid=True, softmax=True, other_act is not None].")
+
+        self.include_background = include_background
+        self.to_onehot_y = to_onehot_y
+        self.sigmoid = sigmoid
+        self.softmax = softmax
+        self.other_act = other_act
+        self.batch = batch
+
+    @torch.no_grad()
+    def compute_distance_map(self, target: torch.Tensor) -> torch.Tensor:
+        """
+        Compute the signed distance map for each class in the target.
+
+        The signed distance map is negative inside the foreground region and positive outside,
+        with zero on the boundary.
+
+        Args:
+            target: target tensor of shape BNHW[D], with values in {0, 1} (one-hot encoded).
+
+        Returns:
+            Signed distance map of the same shape as target.
+        """
+        if target.dim() not in (4, 5):
+            raise ValueError("Only 2D (BNHW) and 3D (BNHWD) supported")
+
+        distance_map = torch.zeros_like(target, dtype=torch.float32)
+
+        for batch_idx in range(target.shape[0]):
+            for channel_idx in range(target.shape[1]):
+                mask = target[batch_idx, channel_idx : channel_idx + 1] > 0.5
+
+                # Empty or full masks do not have a foreground/background interface.
+                if not mask.any() or mask.all():
+                    continue
+
+                fg_dist: torch.Tensor = distance_transform_edt(mask)  # type: ignore
+                bg_dist: torch.Tensor = distance_transform_edt(~mask)  # type: ignore
+
+                signed = torch.zeros_like(mask, dtype=torch.float32)
+                signed[mask] = -(fg_dist[mask].to(torch.float32) - 1)
+                signed[~mask] = bg_dist[~mask].to(torch.float32)
+
+                distance_map[batch_idx, channel_idx] = signed[0]
+
+        return distance_map
+
+    def forward(self, input: torch.Tensor, target: torch.Tensor) -> torch.Tensor:
+        """
+        Args:
+            input: the shape should be BNHW[D], where N is the number of classes.
+            target: the shape should be BNHW[D] or B1HW[D], where N is the number of classes.
+
+        Raises:
+            ValueError: If the input is not 2D (BNHW) or 3D (BNHWD).
+            AssertionError: When input and target (after one hot transform if set)
+                have different shapes.
+            ValueError: When ``self.reduction`` is not one of ["mean", "sum", "none"].
+
+        Example:
+            >>> import torch
+            >>> from monai.losses import BoundaryLoss
+            >>> B, C, H, W = 2, 3, 5, 5
+            >>> input = torch.rand(B, C, H, W)
+            >>> target_idx = torch.randint(0, C, size=(B, H, W)).long()
+            >>> target = one_hot(target_idx[:, None, ...], num_classes=C)
+            >>> bl = BoundaryLoss(softmax=True)
+            >>> loss = bl(input, target)
+        """
+        if input.dim() not in (4, 5):
+            raise ValueError("Only 2D (BNHW) and 3D (BNHWD) supported")
+
+        n_pred_ch = input.shape[1]
+
+        # Apply activation to input
+        if self.sigmoid:
+            input = torch.sigmoid(input)
+
+        if self.softmax:
+            if n_pred_ch == 1:
+                warnings.warn("single channel prediction, `softmax=True` ignored.", stacklevel=2)
+            else:
+                input = torch.softmax(input, dim=1)
+
+        if self.other_act is not None:
+            input = self.other_act(input)
+
+        # Convert target to one-hot if needed
+        if self.to_onehot_y:
+            if n_pred_ch == 1:
+                warnings.warn("single channel prediction, `to_onehot_y=True` ignored.", stacklevel=2)
+            else:
+                if target.dim() == input.dim() - 1:
+                    target = target.unsqueeze(dim=1)
+                target = one_hot(target, num_classes=n_pred_ch)
+
+        # Validate shapes match
+        if input.shape != target.shape:
+            raise AssertionError(f"input and target shapes do not match: {input.shape} vs {target.shape}")
+
+        # Exclude background if requested
+        if not self.include_background:
+            if n_pred_ch == 1:
+                warnings.warn("single channel prediction, `include_background=False` ignored.", stacklevel=2)
+            else:
+                input = input[:, 1:]
+                target = target[:, 1:]
+
+        # Compute signed distance maps from target
+        distance_map = self.compute_distance_map(target)
+
+        # Compute boundary loss: sum over spatial dimensions of (probabilities * distance_map)
+        # Then average over classes and batch
+        spatial_axes = list(range(2, input.dim()))
+
+        loss = torch.sum(input * distance_map, dim=spatial_axes)
+
+        # Normalize by number of pixels per class per batch element
+        num_pixels = torch.prod(torch.as_tensor(input.shape[2:], device=input.device))
+        loss = loss / num_pixels
+        if self.batch:
+            loss = loss.mean(dim=0)
+
+        if self.reduction == LossReduction.MEAN.value:
+            loss = loss.mean()
+        elif self.reduction == LossReduction.SUM.value:
+            loss = loss.sum()
+        elif self.reduction == LossReduction.NONE.value:
+            # Return shape (B, C') unless batch=True reduces the batch dimension first.
+            pass
+        else:
+            raise ValueError(f"Unsupported reduction: {self.reduction}")
+
+        return loss

{monai_weekly-1.7.dev2627 → monai_weekly-1.7.dev2629}/monai/networks/blocks/__init__.py

@@ -26,6 +26,13 @@ from .dynunet_block import UnetBasicBlock, UnetOutBlock, UnetResBlock, UnetUpBlo
 from .encoder import BaseEncoder
 from .fcn import FCN, GCN, MCFCN, Refine
 from .feature_pyramid_network import ExtraFPNBlock, FeaturePyramidNetwork, LastLevelMaxPool, LastLevelP6P7
+from .hyena import (
+    DepthwiseFFTConv2d,
+    DepthwiseFFTConv3d,
+    HyenaMixer,
+    HyenaTransformerBlock,
+    is_nvsubquadratic_available,
+)
 from .localnet_block import LocalNetDownSampleBlock, LocalNetFeatureExtractorBlock, LocalNetUpSampleBlock
 from .mednext_block import MedNeXtBlock, MedNeXtDownBlock, MedNeXtOutBlock, MedNeXtUpBlock
 from .mlp import MLPBlock