feat: add clDice loss (#6763)

SauravMaheshkar · web-flow · commit 2800a76764bc · 2023-07-25T10:28:25.000+01:00
Fixes #5938 ### Description This PR aims to add the `SoftclDiceLoss` and the `SoftDiceclDiceLoss` from [clDice - a Novel Topology-Preserving Loss Function for Tubular Structure Segmentation](https://openaccess.thecvf.com/content/CVPR2021/papers/Shit_clDice_-_A_Novel_Topology-Preserving_Loss_Function_for_Tubular_Structure_CVPR_2021_paper.pdf) ### Types of changes  - [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). - [x] 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`. - [x] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Saurav Maheshkar <sauravvmaheshkar@gmail.com>
diff --git a/monai/losses/__init__.py b/monai/losses/__init__.py
@@ -11,6 +11,7 @@
 
 from __future__ import annotations
 
+from .cldice import SoftclDiceLoss, SoftDiceclDiceLoss
 from .contrastive import ContrastiveLoss
 from .deform import BendingEnergyLoss
 from .dice import (
diff --git a/monai/losses/cldice.py b/monai/losses/cldice.py
@@ -0,0 +1,184 @@
+# 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 torch
+import torch.nn.functional as F
+from torch.nn.modules.loss import _Loss
+
+
+def soft_erode(img: torch.Tensor) -> torch.Tensor:  # type: ignore
+    """
+    Perform soft erosion on the input image
+
+    Args:
+        img: the shape should be BCH(WD)
+
+    Adapted from:
+        https://github.com/jocpae/clDice/blob/master/cldice_loss/pytorch/soft_skeleton.py#L6
+    """
+    if len(img.shape) == 4:
+        p1 = -(F.max_pool2d(-img, (3, 1), (1, 1), (1, 0)))
+        p2 = -(F.max_pool2d(-img, (1, 3), (1, 1), (0, 1)))
+        return torch.min(p1, p2)  # type: ignore
+    elif len(img.shape) == 5:
+        p1 = -(F.max_pool3d(-img, (3, 1, 1), (1, 1, 1), (1, 0, 0)))
+        p2 = -(F.max_pool3d(-img, (1, 3, 1), (1, 1, 1), (0, 1, 0)))
+        p3 = -(F.max_pool3d(-img, (1, 1, 3), (1, 1, 1), (0, 0, 1)))
+        return torch.min(torch.min(p1, p2), p3)  # type: ignore
+
+
+def soft_dilate(img: torch.Tensor) -> torch.Tensor:  # type: ignore
+    """
+    Perform soft dilation on the input image
+
+    Args:
+        img: the shape should be BCH(WD)
+
+    Adapted from:
+        https://github.com/jocpae/clDice/blob/master/cldice_loss/pytorch/soft_skeleton.py#L18
+    """
+    if len(img.shape) == 4:
+        return F.max_pool2d(img, (3, 3), (1, 1), (1, 1))  # type: ignore
+    elif len(img.shape) == 5:
+        return F.max_pool3d(img, (3, 3, 3), (1, 1, 1), (1, 1, 1))  # type: ignore
+
+
+def soft_open(img: torch.Tensor) -> torch.Tensor:
+    """
+    Wrapper function to perform soft opening on the input image
+
+    Args:
+        img: the shape should be BCH(WD)
+
+    Adapted from:
+        https://github.com/jocpae/clDice/blob/master/cldice_loss/pytorch/soft_skeleton.py#L25
+    """
+    eroded_image = soft_erode(img)
+    dilated_image = soft_dilate(eroded_image)
+    return dilated_image
+
+
+def soft_skel(img: torch.Tensor, iter_: int) -> torch.Tensor:
+    """
+    Perform soft skeletonization on the input image
+
+    Adapted from:
+       https://github.com/jocpae/clDice/blob/master/cldice_loss/pytorch/soft_skeleton.py#L29
+
+    Args:
+        img: the shape should be BCH(WD)
+        iter_: number of iterations for skeletonization
+
+    Returns:
+        skeletonized image
+    """
+    img1 = soft_open(img)
+    skel = F.relu(img - img1)
+    for _ in range(iter_):
+        img = soft_erode(img)
+        img1 = soft_open(img)
+        delta = F.relu(img - img1)
+        skel = skel + F.relu(delta - skel * delta)
+    return skel
+
+
+def soft_dice(y_true: torch.Tensor, y_pred: torch.Tensor, smooth: float = 1.0) -> torch.Tensor:
+    """
+    Function to compute soft dice loss
+
+    Adapted from:
+        https://github.com/jocpae/clDice/blob/master/cldice_loss/pytorch/cldice.py#L22
+
+    Args:
+        y_true: the shape should be BCH(WD)
+        y_pred: the shape should be BCH(WD)
+
+    Returns:
+        dice loss
+    """
+    intersection = torch.sum((y_true * y_pred)[:, 1:, ...])
+    coeff = (2.0 * intersection + smooth) / (torch.sum(y_true[:, 1:, ...]) + torch.sum(y_pred[:, 1:, ...]) + smooth)
+    soft_dice: torch.Tensor = 1.0 - coeff
+    return soft_dice
+
+
+class SoftclDiceLoss(_Loss):
+    """
+    Compute the Soft clDice loss defined in:
+
+        Shit et al. (2021) clDice -- A Novel Topology-Preserving Loss Function
+        for Tubular Structure Segmentation. (https://arxiv.org/abs/2003.07311)
+
+    Adapted from:
+        https://github.com/jocpae/clDice/blob/master/cldice_loss/pytorch/cldice.py#L7
+    """
+
+    def __init__(self, iter_: int = 3, smooth: float = 1.0) -> None:
+        """
+        Args:
+            iter_: Number of iterations for skeletonization
+            smooth: Smoothing parameter
+        """
+        super().__init__()
+        self.iter = iter_
+        self.smooth = smooth
+
+    def forward(self, y_true: torch.Tensor, y_pred: torch.Tensor) -> torch.Tensor:
+        skel_pred = soft_skel(y_pred, self.iter)
+        skel_true = soft_skel(y_true, self.iter)
+        tprec = (torch.sum(torch.multiply(skel_pred, y_true)[:, 1:, ...]) + self.smooth) / (
+            torch.sum(skel_pred[:, 1:, ...]) + self.smooth
+        )
+        tsens = (torch.sum(torch.multiply(skel_true, y_pred)[:, 1:, ...]) + self.smooth) / (
+            torch.sum(skel_true[:, 1:, ...]) + self.smooth
+        )
+        cl_dice: torch.Tensor = 1.0 - 2.0 * (tprec * tsens) / (tprec + tsens)
+        return cl_dice
+
+
+class SoftDiceclDiceLoss(_Loss):
+    """
+    Compute the Soft clDice loss defined in:
+
+        Shit et al. (2021) clDice -- A Novel Topology-Preserving Loss Function
+        for Tubular Structure Segmentation. (https://arxiv.org/abs/2003.07311)
+
+    Adapted from:
+        https://github.com/jocpae/clDice/blob/master/cldice_loss/pytorch/cldice.py#L38
+    """
+
+    def __init__(self, iter_: int = 3, alpha: float = 0.5, smooth: float = 1.0) -> None:
+        """
+        Args:
+            iter_: Number of iterations for skeletonization
+            smooth: Smoothing parameter
+            alpha: Weighing factor for cldice
+        """
+        super().__init__()
+        self.iter = iter_
+        self.smooth = smooth
+        self.alpha = alpha
+
+    def forward(self, y_true: torch.Tensor, y_pred: torch.Tensor) -> torch.Tensor:
+        dice = soft_dice(y_true, y_pred, self.smooth)
+        skel_pred = soft_skel(y_pred, self.iter)
+        skel_true = soft_skel(y_true, self.iter)
+        tprec = (torch.sum(torch.multiply(skel_pred, y_true)[:, 1:, ...]) + self.smooth) / (
+            torch.sum(skel_pred[:, 1:, ...]) + self.smooth
+        )
+        tsens = (torch.sum(torch.multiply(skel_true, y_pred)[:, 1:, ...]) + self.smooth) / (
+            torch.sum(skel_true[:, 1:, ...]) + self.smooth
+        )
+        cl_dice = 1.0 - 2.0 * (tprec * tsens) / (tprec + tsens)
+        total_loss: torch.Tensor = (1.0 - self.alpha) * dice + self.alpha * cl_dice
+        return total_loss
diff --git a/tests/test_cldice_loss.py b/tests/test_cldice_loss.py
@@ -0,0 +1,56 @@
+# 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 unittest
+
+import numpy as np
+import torch
+from parameterized import parameterized
+
+from monai.losses import SoftclDiceLoss, SoftDiceclDiceLoss
+
+TEST_CASES = [
+    [  # shape: (1, 4), (1, 4)
+        {"y_pred": torch.ones((100, 3, 256, 256)), "y_true": torch.ones((100, 3, 256, 256))},
+        0.0,
+    ],
+    [  # shape: (1, 5), (1, 5)
+        {"y_pred": torch.ones((100, 3, 256, 256, 5)), "y_true": torch.ones((100, 3, 256, 256, 5))},
+        0.0,
+    ],
+]
+
+
+class TestclDiceLoss(unittest.TestCase):
+    @parameterized.expand(TEST_CASES)
+    def test_result(self, y_pred_data, expected_val):
+        loss = SoftclDiceLoss()
+        loss_dice = SoftDiceclDiceLoss()
+        result = loss(**y_pred_data)
+        result_dice = loss_dice(**y_pred_data)
+        np.testing.assert_allclose(result.detach().cpu().numpy(), expected_val, atol=1e-4, rtol=1e-4)
+        np.testing.assert_allclose(result_dice.detach().cpu().numpy(), expected_val, atol=1e-4, rtol=1e-4)
+
+    def test_with_cuda(self):
+        loss = SoftclDiceLoss()
+        loss_dice = SoftDiceclDiceLoss()
+        i = torch.ones((100, 3, 256, 256))
+        j = torch.ones((100, 3, 256, 256))
+        if torch.cuda.is_available():
+            i = i.cuda()
+            j = j.cuda()
+        output = loss(i, j)
+        output_dice = loss_dice(i, j)
+        np.testing.assert_allclose(output.detach().cpu().numpy(), 0.0, atol=1e-4, rtol=1e-4)
+        np.testing.assert_allclose(output_dice.detach().cpu().numpy(), 0.0, atol=1e-4, rtol=1e-4)
+
+
+if __name__ == "__main__":
+    unittest.main()
