7263 add diffusion loss (#7272)

kvttt · KumoLiu · web-flow · commit d5585c34fc44 · 2023-12-05T08:46:24.000Z
Fixes #7263. ### Description Add diffusion loss. I also made a [demo notebook](https://github.com/kvttt/deep-atlas/blob/main/diffusion_loss_scale_test.ipynb) to provide some explanations and analyses of diffusion loss. ### 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. - [x] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: kaibo <ktang@unc.edu> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
diff --git a/docs/source/losses.rst b/docs/source/losses.rst
@@ -96,6 +96,11 @@ Registration Losses
 .. autoclass:: BendingEnergyLoss
     :members:
 
+`DiffusionLoss`
+~~~~~~~~~~~~~~~
+.. autoclass:: DiffusionLoss
+    :members:
+
 `LocalNormalizedCrossCorrelationLoss`
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: LocalNormalizedCrossCorrelationLoss
diff --git a/monai/losses/__init__.py b/monai/losses/__init__.py
@@ -14,7 +14,7 @@
 from .adversarial_loss import PatchAdversarialLoss
 from .cldice import SoftclDiceLoss, SoftDiceclDiceLoss
 from .contrastive import ContrastiveLoss
-from .deform import BendingEnergyLoss
+from .deform import BendingEnergyLoss, DiffusionLoss
 from .dice import (
     Dice,
     DiceCELoss,
diff --git a/monai/losses/deform.py b/monai/losses/deform.py
@@ -116,3 +116,85 @@ def forward(self, pred: torch.Tensor) -> torch.Tensor:
             raise ValueError(f'Unsupported reduction: {self.reduction}, available options are ["mean", "sum", "none"].')
 
         return energy
+
+
+class DiffusionLoss(_Loss):
+    """
+    Calculate the diffusion based on first-order differentiation of pred using central finite difference.
+    For the original paper, please refer to
+    VoxelMorph: A Learning Framework for Deformable Medical Image Registration,
+    Guha Balakrishnan, Amy Zhao, Mert R. Sabuncu, John Guttag, Adrian V. Dalca
+    IEEE TMI: Transactions on Medical Imaging. 2019. eprint arXiv:1809.05231.
+
+    Adapted from:
+        VoxelMorph (https://github.com/voxelmorph/voxelmorph)
+    """
+
+    def __init__(self, normalize: bool = False, reduction: LossReduction | str = LossReduction.MEAN) -> None:
+        """
+        Args:
+            normalize:
+                Whether to divide out spatial sizes in order to make the computation roughly
+                invariant to image scale (i.e. vector field sampling resolution). Defaults to False.
+            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.
+        """
+        super().__init__(reduction=LossReduction(reduction).value)
+        self.normalize = normalize
+
+    def forward(self, pred: torch.Tensor) -> torch.Tensor:
+        """
+        Args:
+            pred:
+                Predicted dense displacement field (DDF) with shape BCH[WD],
+                where C is the number of spatial dimensions.
+                Note that diffusion loss can only be calculated
+                when the sizes of the DDF along all spatial dimensions are greater than 2.
+
+        Raises:
+            ValueError: When ``self.reduction`` is not one of ["mean", "sum", "none"].
+            ValueError: When ``pred`` is not 3-d, 4-d or 5-d.
+            ValueError: When any spatial dimension of ``pred`` has size less than or equal to 2.
+            ValueError: When the number of channels of ``pred`` does not match the number of spatial dimensions.
+
+        """
+        if pred.ndim not in [3, 4, 5]:
+            raise ValueError(f"Expecting 3-d, 4-d or 5-d pred, instead got pred of shape {pred.shape}")
+        for i in range(pred.ndim - 2):
+            if pred.shape[-i - 1] <= 2:
+                raise ValueError(f"All spatial dimensions must be > 2, got spatial dimensions {pred.shape[2:]}")
+        if pred.shape[1] != pred.ndim - 2:
+            raise ValueError(
+                f"Number of vector components, i.e. number of channels of the input DDF, {pred.shape[1]}, "
+                f"does not match number of spatial dimensions, {pred.ndim - 2}"
+            )
+
+        # first order gradient
+        first_order_gradient = [spatial_gradient(pred, dim) for dim in range(2, pred.ndim)]
+
+        # spatial dimensions in a shape suited for broadcasting below
+        if self.normalize:
+            spatial_dims = torch.tensor(pred.shape, device=pred.device)[2:].reshape((1, -1) + (pred.ndim - 2) * (1,))
+
+        diffusion = torch.tensor(0)
+        for dim_1, g in enumerate(first_order_gradient):
+            dim_1 += 2
+            if self.normalize:
+                # We divide the partial derivative for each vector component at each voxel by the spatial size
+                # corresponding to that component relative to the spatial size of the vector component with respect
+                # to which the partial derivative is taken.
+                g *= pred.shape[dim_1] / spatial_dims
+            diffusion = diffusion + g**2
+
+        if self.reduction == LossReduction.MEAN.value:
+            diffusion = torch.mean(diffusion)  # the batch and channel average
+        elif self.reduction == LossReduction.SUM.value:
+            diffusion = torch.sum(diffusion)  # sum over the batch and channel dims
+        elif self.reduction != LossReduction.NONE.value:
+            raise ValueError(f'Unsupported reduction: {self.reduction}, available options are ["mean", "sum", "none"].')
+
+        return diffusion
diff --git a/tests/test_diffusion_loss.py b/tests/test_diffusion_loss.py
@@ -0,0 +1,116 @@
+# 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 unittest
+
+import numpy as np
+import torch
+from parameterized import parameterized
+
+from monai.losses.deform import DiffusionLoss
+
+device = "cuda" if torch.cuda.is_available() else "cpu"
+
+TEST_CASES = [
+    # all first partials are zero, so the diffusion loss is also zero
+    [{}, {"pred": torch.ones((1, 3, 5, 5, 5), device=device)}, 0.0],
+    # all first partials are one, so the diffusion loss is also one
+    [{}, {"pred": torch.arange(0, 5, device=device)[None, None, None, None, :].expand(1, 3, 5, 5, 5)}, 1.0],
+    # before expansion, the first partials are 2, 4, 6, so the diffusion loss is (2^2 + 4^2 + 6^2) / 3 = 18.67
+    [
+        {"normalize": False},
+        {"pred": torch.arange(0, 5, device=device)[None, None, None, None, :].expand(1, 3, 5, 5, 5) ** 2},
+        56.0 / 3.0,
+    ],
+    # same as the previous case
+    [
+        {"normalize": False},
+        {"pred": torch.arange(0, 5, device=device)[None, None, None, :].expand(1, 2, 5, 5) ** 2},
+        56.0 / 3.0,
+    ],
+    # same as the previous case
+    [{"normalize": False}, {"pred": torch.arange(0, 5, device=device)[None, None, :].expand(1, 1, 5) ** 2}, 56.0 / 3.0],
+    # we have shown in the demo notebook that
+    # diffusion loss is scale-invariant when the all axes have the same resolution
+    [
+        {"normalize": True},
+        {"pred": torch.arange(0, 5, device=device)[None, None, None, None, :].expand(1, 3, 5, 5, 5) ** 2},
+        56.0 / 3.0,
+    ],
+    [
+        {"normalize": True},
+        {"pred": torch.arange(0, 5, device=device)[None, None, None, :].expand(1, 2, 5, 5) ** 2},
+        56.0 / 3.0,
+    ],
+    [{"normalize": True}, {"pred": torch.arange(0, 5, device=device)[None, None, :].expand(1, 1, 5) ** 2}, 56.0 / 3.0],
+    # for the following case, consider the following 2D matrix:
+    # tensor([[[[0, 1, 2],
+    #           [1, 2, 3],
+    #           [2, 3, 4],
+    #           [3, 4, 5],
+    #           [4, 5, 6]],
+    #          [[0, 1, 2],
+    #           [1, 2, 3],
+    #           [2, 3, 4],
+    #           [3, 4, 5],
+    #           [4, 5, 6]]]])
+    # the first partials wrt x are all ones, and so are the first partials wrt y
+    # the diffusion loss, when normalization is not applied, is 1^2 + 1^2 = 2
+    [{"normalize": False}, {"pred": torch.stack([torch.arange(i, i + 3) for i in range(5)]).expand(1, 2, 5, 3)}, 2.0],
+    # consider the same matrix, this time with normalization applied, using the same notation as in the demo notebook,
+    # the coefficients to be divided out are (1, 5/3) for partials wrt x and (3/5, 1) for partials wrt y
+    # the diffusion loss is then (1/1)^2 + (1/(5/3))^2 + (1/(3/5))^2 + (1/1)^2 = (1 + 9/25 + 25/9 + 1) / 2 = 2.5689
+    [
+        {"normalize": True},
+        {"pred": torch.stack([torch.arange(i, i + 3) for i in range(5)]).expand(1, 2, 5, 3)},
+        (1.0 + 9.0 / 25.0 + 25.0 / 9.0 + 1.0) / 2.0,
+    ],
+]
+
+
+class TestDiffusionLoss(unittest.TestCase):
+    @parameterized.expand(TEST_CASES)
+    def test_shape(self, input_param, input_data, expected_val):
+        result = DiffusionLoss(**input_param).forward(**input_data)
+        np.testing.assert_allclose(result.detach().cpu().numpy(), expected_val, rtol=1e-5)
+
+    def test_ill_shape(self):
+        loss = DiffusionLoss()
+        # not in 3-d, 4-d, 5-d
+        with self.assertRaisesRegex(ValueError, "Expecting 3-d, 4-d or 5-d"):
+            loss.forward(torch.ones((1, 3), device=device))
+        with self.assertRaisesRegex(ValueError, "Expecting 3-d, 4-d or 5-d"):
+            loss.forward(torch.ones((1, 4, 5, 5, 5, 5), device=device))
+        with self.assertRaisesRegex(ValueError, "All spatial dimensions"):
+            loss.forward(torch.ones((1, 3, 2, 5, 5), device=device))
+        with self.assertRaisesRegex(ValueError, "All spatial dimensions"):
+            loss.forward(torch.ones((1, 3, 5, 2, 5)))
+        with self.assertRaisesRegex(ValueError, "All spatial dimensions"):
+            loss.forward(torch.ones((1, 3, 5, 5, 2)))
+
+        # number of vector components unequal to number of spatial dims
+        with self.assertRaisesRegex(ValueError, "Number of vector components"):
+            loss.forward(torch.ones((1, 2, 5, 5, 5)))
+        with self.assertRaisesRegex(ValueError, "Number of vector components"):
+            loss.forward(torch.ones((1, 2, 5, 5, 5)))
+
+    def test_ill_opts(self):
+        pred = torch.rand(1, 3, 5, 5, 5).to(device=device)
+        with self.assertRaisesRegex(ValueError, ""):
+            DiffusionLoss(reduction="unknown")(pred)
+        with self.assertRaisesRegex(ValueError, ""):
+            DiffusionLoss(reduction=None)(pred)
+
+
+if __name__ == "__main__":
+    unittest.main()
