Implementation of boundary-aware ShapeLoss

docs/source/losses.rst

@@ -68,6 +68,11 @@ Segmentation Losses
 .. autoclass:: ContrastiveLoss
     :members:
 
+`ShapeLoss`
+~~~~~~~~~~~~~~~~~
+.. autoclass:: ShapeLoss
+    :members:
+
 Registration Losses
 -------------------
 

monai/losses/__init__.py

@@ -27,5 +27,6 @@
 from .focal_loss import FocalLoss
 from .image_dissimilarity import GlobalMutualInformationLoss, LocalNormalizedCrossCorrelationLoss
 from .multi_scale import MultiScaleLoss
+from .shape import ShapeDistLoss
 from .spatial_mask import MaskedLoss
 from .tversky import TverskyLoss

monai/losses/shape.py

@@ -0,0 +1,173 @@
+# 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.
+
+import warnings
+from itertools import product
+from typing import Callable, Optional, Union
+
+import numpy as np
+import torch
+from torch.nn.modules.loss import _Loss
+
+from monai.networks import one_hot
+from monai.utils import LossReduction, convert_data_type, optional_import
+
+distance_transform_edt, _ = optional_import("scipy.ndimage", name="distance_transform_edt")
+
+
+class ShapeDistLoss(_Loss):
+    def __init__(
+        self,
+        include_background: bool = True,
+        to_onehot_y: bool = False,
+        sigmoid: bool = False,
+        softmax: bool = False,
+        other_act: Optional[Callable] = None,
+        smooth_nr: float = 1e-8,
+        smooth_k: float = 2e-1,
+        reduction: Union[LossReduction, str] = LossReduction.MEAN,
+    ) -> None:
+        """
+        Shape Information Loss inspired by [Huang et al., 2021](https://ieeexplore.ieee.org/document/9433775)
+
+        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 `y` into the one-hot format. 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: if don't want to use `sigmoid` or `softmax`, use other callable function to execute
+                other activation layers, Defaults to ``None``. for example:
+                `other_act = torch.tanh`.
+            smooth_nr: a small constant added to the numerator to avoid zero.
+            smooth_k: smoothness factor used in the Heaviside function
+            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.
+
+        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.smooth_nr = float(smooth_nr)
+        self.smooth_k = float(smooth_k)
+
+    def distance_map(self, mask: torch.Tensor) -> torch.Tensor:
+        """Creates a distance map from a 2D binary mask.
+
+        Args:
+            mask (torch.Tensor): Binary mask of shape [WD].
+
+        Returns:
+            torch.Tensor: Boundary distance map of shape [WD]
+        """
+        # Convert to NumPy to use with SciPy
+        roi, _, _ = convert_data_type(mask, np.ndarray)
+
+        # Compute normalized distance transform
+        dt: np.ndarray = distance_transform_edt(roi)
+        dt /= dt.max() + self.smooth_nr
+
+        # apply Heaviside function to softly normalize into [0, 1]
+        result: np.ndarray = 1 / (1 + np.exp(-(1 - dt) / self.smooth_k))
+        # mask using region of interest
+        result *= roi
+
+        return torch.Tensor(result)
+
+    def forward(self, input: torch.Tensor, target: torch.Tensor) -> torch.Tensor:
+        """
+        Args:
+            input: the shape should be BNH[WD], where N is the number of classes.
+            target: the shape should be BNH[WD] or B1H[WD], where N is the number of classes.
+
+        Raises:
+            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:
+            >>> from monai.losses.dice import *  # NOQA
+            >>> import torch
+            >>> from monai.losses.dice import ShapeLoss
+            >>> B, C, H, W = 7, 5, 3, 2
+            >>> input = torch.rand(B, C, H, W)
+            >>> target_idx = torch.randint(low=0, high=C - 1, size=(B, H, W)).long()
+            >>> target = one_hot(target_idx[:, None, ...], num_classes=C)
+            >>> self = ShapeLoss(reduction='none')
+            >>> loss = self(input, target)
+            >>> assert np.broadcast_shapes(loss.shape, input.shape) == input.shape
+        """
+        if self.sigmoid:
+            input = torch.sigmoid(input)
+
+        n_pred_ch = input.shape[1]
+        if self.softmax:
+            if n_pred_ch == 1:
+                warnings.warn("single channel prediction, `softmax=True` ignored.")
+            else:
+                input = torch.softmax(input, 1)
+
+        if self.other_act is not None:
+            input = self.other_act(input)
+
+        if self.to_onehot_y:
+            if n_pred_ch == 1:
+                warnings.warn("single channel prediction, `to_onehot_y=True` ignored.")
+            else:
+                target = one_hot(target, num_classes=n_pred_ch)
+
+        if not self.include_background:
+            if n_pred_ch == 1:
+                warnings.warn("single channel prediction, `include_background=False` ignored.")
+            else:
+                # if skipping background, removing first channel
+                target = target[:, 1:]
+                input = input[:, 1:]
+
+        if target.shape != input.shape:
+            raise AssertionError(f"ground truth has different shape ({target.shape}) from input ({input.shape})")
+
+        distance_maps = torch.empty(size=target.size()).to(input.device)
+
+        for im, ch in product(*map(range, target.shape[:2])):
+            distance_maps[im, ch] = self.distance_map(target[im, ch])
+
+        f = (distance_maps - input).abs().sum(dim=(2, 3)) / input.sum(dim=(2, 3))
+
+        if self.reduction == LossReduction.MEAN.value:
+            f = torch.mean(f)  # the batch and channel average
+        elif self.reduction == LossReduction.SUM.value:
+            f = torch.sum(f)  # sum over the batch and channel dims
+        elif self.reduction == LossReduction.NONE.value:
+            # If we are not computing voxelwise loss components at least
+            # make sure a none reduction maintains a broadcastable shape
+            broadcast_shape = list(f.shape[0:2]) + [1] * (len(input.shape) - 2)
+            f = f.view(broadcast_shape)
+        else:
+            raise ValueError(f'Unsupported reduction: {self.reduction}, available options are ["mean", "sum", "none"].')
+
+        return f