Merge branch 'dev' into fix/pydicom-affine-single-slice-zero-div

ericspod · web-flow · commit a8da81717b18 · 2026-07-05T01:19:26.000-02:30
diff --git a/docs/source/metrics.rst b/docs/source/metrics.rst
@@ -116,6 +116,13 @@ Metrics
 .. autoclass:: SurfaceDiceMetric
     :members:
 
+`Absolute volume difference`
+----------------------------
+.. autofunction:: compute_absolute_volume_difference
+
+.. autoclass:: AbsoluteVolumeDifferenceMetric
+    :members:
+
 `PanopticQualityMetric`
 -----------------------
 .. autofunction:: compute_panoptic_quality
diff --git a/monai/metrics/__init__.py b/monai/metrics/__init__.py
@@ -11,6 +11,7 @@
 
 from __future__ import annotations
 
+from .absolute_volume_difference import AbsoluteVolumeDifferenceMetric, compute_absolute_volume_difference
 from .active_learning_metrics import LabelQualityScore, VarianceMetric, compute_variance, label_quality_score
 from .average_precision import AveragePrecisionMetric, compute_average_precision
 from .calibration import CalibrationErrorMetric, CalibrationReduction, calibration_binning
diff --git a/monai/metrics/absolute_volume_difference.py b/monai/metrics/absolute_volume_difference.py
@@ -0,0 +1,180 @@
+# 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
+
+from monai.metrics.utils import do_metric_reduction, ignore_background
+from monai.utils import MetricReduction
+
+from .metric import CumulativeIterationMetric
+
+__all__ = ["AbsoluteVolumeDifferenceMetric", "compute_absolute_volume_difference"]
+
+
+class AbsoluteVolumeDifferenceMetric(CumulativeIterationMetric):
+    """
+    Compute the Absolute Volume Difference (AVD) between predicted and ground-truth
+    segmentation masks.
+
+    AVD measures the absolute difference in the number of foreground voxels between
+    prediction and ground truth, per class.  It is particularly useful for small-object
+    segmentation (e.g. retinal fluid in OCT volumes) where Dice score is known to be
+    overly sensitive to volume size and does not directly reflect volume discrepancies.
+
+    .. note::
+        For 2D inputs this computes the difference in foreground **areas** rather than
+        volumes.  In all cases the returned values are raw voxel/pixel counts and are
+        **not** scaled by the voxel/pixel spacing, so they are not expressed in the
+        physical units of the original image.
+
+    Reference:
+        Bogunovic et al. (2019). RETOUCH: The Retinal OCT Fluid Detection and
+        Segmentation Benchmark and Challenge.
+        IEEE Transactions on Medical Imaging, 38(8), 1858-1874.
+        https://ieeexplore.ieee.org/document/8653407
+
+    The inputs ``y_pred`` and ``y`` are expected to be binarized one-hot tensors with
+    shape BCHW[D].  If they contain continuous values (e.g. sigmoid outputs), binarize
+    them first with a suitable threshold transform.
+
+    The typical execution steps of this metric class follow
+    :py:class:`monai.metrics.metric.Cumulative`.
+
+    Example:
+
+    .. code-block:: python
+
+        import torch
+        from monai.metrics import AbsoluteVolumeDifferenceMetric
+
+        batch_size, n_classes = 4, 3
+        y_pred = torch.randint(0, 2, (batch_size, n_classes, 64, 64, 32)).float()
+        y      = torch.randint(0, 2, (batch_size, n_classes, 64, 64, 32)).float()
+
+        metric = AbsoluteVolumeDifferenceMetric(include_background=False)
+        metric(y_pred, y)                 # accumulate
+        result = metric.aggregate()       # shape: (n_classes - 1,) after mean reduction
+        metric.reset()
+
+    Args:
+        include_background: whether to include AVD computation on the first channel
+            (index 0), which is by convention assumed to be background.  Defaults to
+            ``True``.  Set to ``False`` when the background class dominates and you only
+            care about foreground classes (e.g. fluid sub-types in OCT).
+        reduction: defines how to aggregate per-batch-per-class results.  Available
+            modes are enumerated in :py:class:`monai.utils.enums.MetricReduction`.
+            Defaults to ``"mean"``.
+        get_not_nans: if ``True``, :meth:`aggregate` returns ``(metric, not_nans)``
+            where ``not_nans`` counts the number of valid (non-NaN) values.
+            Defaults to ``False``.
+        ignore_empty: if ``True``, cases where the ground-truth channel is entirely
+            empty (zero voxels) are excluded from aggregation by setting their value
+            to ``NaN``.  If ``False``, the raw absolute difference (equal to the
+            predicted volume for that class) is returned.  Defaults to ``True``.
+    """
+
+    def __init__(
+        self,
+        include_background: bool = True,
+        reduction: MetricReduction | str = MetricReduction.MEAN,
+        get_not_nans: bool = False,
+        ignore_empty: bool = True,
+    ) -> None:
+        super().__init__()
+        self.include_background = include_background
+        self.reduction = reduction
+        self.get_not_nans = get_not_nans
+        self.ignore_empty = ignore_empty
+
+    def _compute_tensor(self, y_pred: torch.Tensor, y: torch.Tensor) -> torch.Tensor:  # type: ignore[override]
+        """
+        Args:
+            y_pred: binarized prediction tensor, shape BCHW[D].
+            y: binarized ground-truth tensor, shape BCHW[D].
+
+        Raises:
+            ValueError: when ``y_pred`` has fewer than three dimensions.
+        """
+        if y_pred.ndimension() < 3:
+            raise ValueError(
+                f"y_pred should have at least 3 dimensions (batch, channel, spatial), got {y_pred.ndimension()}."
+            )
+        return compute_absolute_volume_difference(
+            y_pred=y_pred, y=y, include_background=self.include_background, ignore_empty=self.ignore_empty
+        )
+
+    def aggregate(
+        self, reduction: MetricReduction | str | None = None
+    ) -> torch.Tensor | tuple[torch.Tensor, torch.Tensor]:
+        """
+        Execute reduction logic for the accumulated AVD values.
+
+        Args:
+            reduction: optional override for the reduction mode set at construction.
+        """
+        data = self.get_buffer()
+        if not isinstance(data, torch.Tensor):
+            raise ValueError("the data to aggregate must be a PyTorch Tensor.")
+
+        f, not_nans = do_metric_reduction(data, reduction or self.reduction)
+        return (f, not_nans) if self.get_not_nans else f
+
+
+def compute_absolute_volume_difference(
+    y_pred: torch.Tensor, y: torch.Tensor, include_background: bool = True, ignore_empty: bool = True
+) -> torch.Tensor:
+    """
+    Compute the Absolute Volume Difference (AVD) for a batch of segmentation predictions.
+
+    AVD is defined per class as::
+
+        AVD_c = | sum_{spatial}(y_pred_c) - sum_{spatial}(y_c) |
+
+    where the sum counts the number of foreground voxels in each channel.
+
+    Args:
+        y_pred: binarized prediction tensor with shape BCHW[D].
+        y: binarized ground-truth tensor with shape BCHW[D].
+        include_background: whether to include the first channel (background).
+            Defaults to ``True``.
+        ignore_empty: if ``True``, entries where the ground-truth channel contains no
+            foreground voxels are set to ``NaN`` so they are excluded during reduction.
+            Defaults to ``True``.
+
+    Returns:
+        AVD per batch item and per class, shape ``[batch_size, num_classes]``.
+
+    Raises:
+        ValueError: when ``y_pred`` and ``y`` have different shapes.
+    """
+    if y_pred.ndim < 3:
+        raise ValueError(f"y_pred should have at least 3 dimensions (batch, channel, spatial), got {y_pred.ndim}.")
+
+    if not include_background:
+        y_pred, y = ignore_background(y_pred=y_pred, y=y)
+
+    if y_pred.shape != y.shape:
+        raise ValueError(f"y_pred and y should have the same shape, got {y_pred.shape} and {y.shape}.")
+
+    # sum over all spatial dimensions; keep batch (dim 0) and channel (dim 1)
+    reduce_axis = list(range(2, y_pred.ndim))
+    vol_pred = torch.sum(y_pred, dim=reduce_axis)  # [B, C]
+    vol_true = torch.sum(y, dim=reduce_axis)  # [B, C]
+
+    avd = torch.abs(vol_pred - vol_true)  # [B, C]
+
+    if ignore_empty:
+        # mark cases with no ground-truth foreground as NaN
+        avd = torch.where(vol_true > 0, avd, torch.tensor(float("nan"), device=avd.device))
+
+    return avd
diff --git a/tests/metrics/test_absolute_volume_difference.py b/tests/metrics/test_absolute_volume_difference.py
@@ -0,0 +1,161 @@
+# 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 torch
+
+from monai.metrics import AbsoluteVolumeDifferenceMetric, compute_absolute_volume_difference
+
+
+class TestComputeAbsoluteVolumeDifference(unittest.TestCase):
+    """Tests for the standalone compute_absolute_volume_difference function."""
+
+    def test_perfect_prediction_returns_zero(self):
+        """Identical prediction and ground truth should yield AVD of zero for all classes."""
+        # identical masks → AVD = 0 for every class
+        y = torch.zeros(2, 3, 4, 4)
+        y[:, 1, :2, :2] = 1.0
+        y[:, 2, 2:, 2:] = 1.0
+        result = compute_absolute_volume_difference(y_pred=y, y=y, ignore_empty=False)
+        self.assertEqual(result.shape, torch.Size([2, 3]))
+        self.assertTrue(torch.all(result == 0.0))
+
+    def test_known_volume_difference(self):
+        """AVD should equal the absolute difference in foreground voxel counts between prediction and GT."""
+        # batch=1, 2 classes (background + foreground), 1D spatial of length 10
+        y_pred = torch.zeros(1, 2, 10)
+        y_true = torch.zeros(1, 2, 10)
+        y_pred[0, 1, :7] = 1.0  # 7 foreground voxels predicted
+        y_true[0, 1, :4] = 1.0  # 4 foreground voxels in GT
+        result = compute_absolute_volume_difference(y_pred=y_pred, y=y_true, ignore_empty=False)
+        # channel 0: both all-zeros → AVD = 0
+        # channel 1: |7 - 4| = 3
+        self.assertAlmostEqual(result[0, 0].item(), 0.0)
+        self.assertAlmostEqual(result[0, 1].item(), 3.0)
+
+    def test_ignore_background(self):
+        """Setting include_background=False should strip the first channel and reduce output shape accordingly."""
+        y_pred = torch.zeros(2, 3, 8, 8)
+        y_true = torch.zeros(2, 3, 8, 8)
+        y_pred[:, 1, :3, :3] = 1.0
+        y_true[:, 1, :4, :4] = 1.0
+        result = compute_absolute_volume_difference(y_pred=y_pred, y=y_true, include_background=False)
+        # background channel stripped → shape [2, 2]
+        self.assertEqual(result.shape, torch.Size([2, 2]))
+
+    def test_ignore_empty_sets_nan(self):
+        """Channels with no ground-truth foreground voxels should be NaN when ignore_empty=True."""
+        # channel 1 has no GT voxels → should be NaN when ignore_empty=True
+        y_pred = torch.zeros(1, 2, 6)
+        y_true = torch.zeros(1, 2, 6)
+        y_pred[0, 0, :3] = 1.0
+        result = compute_absolute_volume_difference(y_pred=y_pred, y=y_true, ignore_empty=True)
+        # channel 0: GT is empty → NaN
+        self.assertTrue(torch.isnan(result[0, 0]))
+        # channel 1: GT is empty → NaN
+        self.assertTrue(torch.isnan(result[0, 1]))
+
+    def test_ignore_empty_false_returns_pred_volume(self):
+        """With ignore_empty=False and empty GT, AVD should equal the predicted volume."""
+        # when GT is all zero and ignore_empty=False, AVD = |V_pred - 0| = V_pred
+        y_pred = torch.zeros(1, 2, 6)
+        y_true = torch.zeros(1, 2, 6)
+        y_pred[0, 1, :5] = 1.0
+        result = compute_absolute_volume_difference(y_pred=y_pred, y=y_true, ignore_empty=False)
+        self.assertAlmostEqual(result[0, 1].item(), 5.0)
+
+    def test_shape_mismatch_raises(self):
+        """Mismatched y_pred and y shapes should raise a ValueError."""
+        with self.assertRaises(ValueError):
+            compute_absolute_volume_difference(y_pred=torch.zeros(2, 3, 8, 8), y=torch.zeros(2, 3, 4, 4))
+
+    def test_too_few_dims_raises(self):
+        """Input tensors with fewer than 3 dimensions should raise a ValueError."""
+        with self.assertRaises(ValueError):
+            compute_absolute_volume_difference(y_pred=torch.zeros(2, 3), y=torch.zeros(2, 3))
+
+    def test_3d_volumes(self):
+        """AVD should correctly count voxel differences in 3-D spatial inputs."""
+        # 3-D spatial (D, H, W)
+        y_pred = torch.zeros(1, 2, 8, 8, 8)
+        y_true = torch.zeros(1, 2, 8, 8, 8)
+        y_pred[0, 1, :4, :4, :4] = 1.0  # 64 voxels
+        y_true[0, 1, :3, :3, :3] = 1.0  # 27 voxels
+        result = compute_absolute_volume_difference(y_pred=y_pred, y=y_true, ignore_empty=False)
+        self.assertAlmostEqual(result[0, 1].item(), 37.0)
+
+    def test_output_shape_multi_class(self):
+        """Output shape should be [batch_size, num_classes] for multi-class inputs."""
+        y = torch.randint(0, 2, (4, 5, 16, 16)).float()
+        result = compute_absolute_volume_difference(y_pred=y, y=y, ignore_empty=False)
+        self.assertEqual(result.shape, torch.Size([4, 5]))
+
+
+class TestAbsoluteVolumeDifferenceMetric(unittest.TestCase):
+    """Tests for the AbsoluteVolumeDifferenceMetric class (cumulative interface)."""
+
+    def test_aggregate_mean(self):
+        """Mean reduction over accumulated batches should return the correct per-class AVD."""
+        y_pred = torch.zeros(2, 2, 8, 8)
+        y_true = torch.zeros(2, 2, 8, 8)
+        y_pred[:, 1, :6, :6] = 1.0  # 36 voxels per batch item
+        y_true[:, 1, :4, :4] = 1.0  # 16 voxels per batch item
+        metric = AbsoluteVolumeDifferenceMetric(include_background=False, reduction="mean", ignore_empty=False)
+        metric(y_pred, y_true)
+        agg = metric.aggregate()
+        # single foreground channel, AVD = 20 for both batch items → mean = 20
+        self.assertAlmostEqual(agg.item(), 20.0)
+        metric.reset()
+
+    def test_aggregate_returns_not_nans_when_requested(self):
+        """When get_not_nans=True, aggregate should return a (metric, not_nans) tuple."""
+        y_pred = torch.zeros(2, 2, 4, 4)
+        y_true = torch.zeros(2, 2, 4, 4)
+        y_pred[:, 1, :2, :2] = 1.0
+        y_true[:, 1, :2, :2] = 1.0
+        metric = AbsoluteVolumeDifferenceMetric(include_background=False, get_not_nans=True)
+        metric(y_pred, y_true)
+        result, not_nans = metric.aggregate()
+        self.assertIsInstance(result, torch.Tensor)
+        self.assertIsInstance(not_nans, torch.Tensor)
+        metric.reset()
+
+    def test_cumulative_accumulation(self):
+        """Multiple forward calls before aggregate should use all accumulated data correctly."""
+        # calling the metric twice and aggregating should use all accumulated data
+        metric = AbsoluteVolumeDifferenceMetric(include_background=False, reduction="mean", ignore_empty=False)
+        for _ in range(3):
+            y_pred = torch.zeros(1, 2, 8)
+            y_true = torch.zeros(1, 2, 8)
+            y_pred[0, 1, :6] = 1.0
+            y_true[0, 1, :4] = 1.0
+            metric(y_pred, y_true)
+        agg = metric.aggregate()
+        self.assertAlmostEqual(agg.item(), 2.0)
+        metric.reset()
+
+    def test_reset_clears_buffer(self):
+        """Calling reset() should clear the buffer so a subsequent aggregate() raises."""
+        metric = AbsoluteVolumeDifferenceMetric(ignore_empty=False)
+        y = torch.zeros(1, 2, 4)
+        y[0, 1, :2] = 1.0
+        metric(y, y)
+        metric.reset()
+        # after reset the buffer should be empty; calling aggregate raises
+        with self.assertRaises(ValueError):
+            metric.aggregate()
+
+
+if __name__ == "__main__":
+    unittest.main()
