Deprecate Dice from classification and re-add to segmentation (#2725)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Jirka Borovec <[email protected]>

CHANGELOG.md

@@ -15,10 +15,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Added `NormalizedRootMeanSquaredError` metric to regression subpackage ([#2442](https://github.com/Lightning-AI/torchmetrics/pull/2442))
 
 
+- Added `Dice` metric to segmentation metrics ([#2725](https://github.com/Lightning-AI/torchmetrics/pull/2725))
+
+
 ### Changed
 
 - Changed naming and input order arguments in `KLDivergence` ([#2800](https://github.com/Lightning-AI/torchmetrics/pull/2800))
 
+### Deprecated
+
+- Deprecated Dice from classification metrics ([#2725](https://github.com/Lightning-AI/torchmetrics/pull/2725))
+
 
 ### Removed
 

docs/source/segmentation/dice.rst

@@ -0,0 +1,22 @@
+.. customcarditem::
+   :header: Score
+   :image: https://pl-flash-data.s3.amazonaws.com/assets/thumbnails/tabular_classification.svg
+   :tags: Segmentation
+
+.. include:: ../links.rst
+
+##########
+Dice Score
+##########
+
+Module Interface
+________________
+
+.. autoclass:: torchmetrics.segmentation.DiceScore
+    :noindex:
+
+Functional Interface
+____________________
+
+.. autofunction:: torchmetrics.functional.segmentation.dice_score
+    :noindex:

src/torchmetrics/classification/dice.py

@@ -20,6 +20,7 @@
 from torchmetrics.functional.classification.dice import _dice_compute
 from torchmetrics.functional.classification.stat_scores import _stat_scores_update
 from torchmetrics.metric import Metric
+from torchmetrics.utilities import rank_zero_warn
 from torchmetrics.utilities.enums import AverageMethod, MDMCAverageMethod
 from torchmetrics.utilities.imports import _MATPLOTLIB_AVAILABLE
 from torchmetrics.utilities.plot import _AX_TYPE, _PLOT_OUT_TYPE
@@ -114,6 +115,12 @@ class Dice(Metric):
 
         kwargs: Additional keyword arguments, see :ref:`Metric kwargs` for more info.
 
+    .. warning::
+        The ``dice`` metrics is being deprecated from the classification subpackage in v1.6.0 of torchmetrics and will
+        be removed in v1.7.0. Please instead consider using ``f1score`` metric from the classification subpackage as it
+        provides the same functionality. Additionally, we are going to re-add the ``dice`` metric in the segmentation
+        domain in v1.6.0 with slight modifications to functionality.
+
     Raises:
         ValueError:
             If ``average`` is none of ``"micro"``, ``"macro"``, ``"samples"``, ``"none"``, ``None``.
@@ -155,6 +162,14 @@ def __init__(
         multiclass: Optional[bool] = None,
         **kwargs: Any,
     ) -> None:
+        rank_zero_warn(
+            "The `dice` metrics is being deprecated from the classification subpackage in v1.6.0 of torchmetrics and"
+            " will removed in v1.7.0. Please instead consider using `f1score` metric from the classification subpackage"
+            " as it provides the same functionality. Additionally, we are going to re-add the `dice` metric in the"
+            " segmentation domain in v1.6.0 with slight modifications to functionality.",
+            DeprecationWarning,
+        )
+
         super().__init__(**kwargs)
         allowed_average = ("micro", "macro", "samples", "none", None)
         if average not in allowed_average:

src/torchmetrics/functional/classification/dice.py

@@ -17,6 +17,7 @@
 from torch import Tensor
 
 from torchmetrics.functional.classification.stat_scores import _reduce_stat_scores, _stat_scores_update
+from torchmetrics.utilities import rank_zero_warn
 from torchmetrics.utilities.checks import _input_squeeze
 from torchmetrics.utilities.enums import AverageMethod, MDMCAverageMethod
 
@@ -150,6 +151,12 @@ def dice(
             Used only in certain special cases, where you want to treat inputs as a different type
             than what they appear to be.
 
+    .. warning::
+        The ``dice`` metrics is being deprecated from the classification subpackage in v1.6.0 of torchmetrics and will
+        be removed in v1.7.0. Please instead consider using ``f1score`` metric from the classification subpackage as it
+        provides the same functionality. Additionally, we are going to re-add the ``dice`` metric in the segmentation
+        domain in v1.6.0 with slight modifications to functionality.
+
     Return:
         The shape of the returned tensor depends on the ``average`` parameter
 
@@ -174,6 +181,14 @@ def dice(
         tensor(0.2500)
 
     """
+    rank_zero_warn(
+        "The `dice` metrics is being deprecated from the classification subpackage in v1.6.0 of torchmetrics and will"
+        " removed in v1.7.0. Please instead consider using `f1score` metric from the classification subpackage as it"
+        " provides the same functionality. Additionally, we are going to re-add the `dice` metric in the segmentation"
+        " domain in v1.6.0 with slight modifications to functionality.",
+        DeprecationWarning,
+    )
+
     allowed_average = ("micro", "macro", "weighted", "samples", "none", None)
     if average not in allowed_average:
         raise ValueError(f"The `average` has to be one of {allowed_average}, got {average}.")

src/torchmetrics/functional/segmentation/__init__.py

@@ -11,8 +11,9 @@
 # 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 torchmetrics.functional.segmentation.dice import dice_score
 from torchmetrics.functional.segmentation.generalized_dice import generalized_dice_score
 from torchmetrics.functional.segmentation.hausdorff_distance import hausdorff_distance
 from torchmetrics.functional.segmentation.mean_iou import mean_iou
 
-__all__ = ["generalized_dice_score", "mean_iou", "hausdorff_distance"]
+__all__ = ["generalized_dice_score", "mean_iou", "hausdorff_distance", "dice_score"]

src/torchmetrics/functional/segmentation/dice.py

@@ -0,0 +1,148 @@
+# Copyright The PyTorch Lightning team.
+#
+# 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 typing import Optional, Tuple
+
+import torch
+from torch import Tensor
+from typing_extensions import Literal
+
+from torchmetrics.functional.segmentation.utils import _ignore_background
+from torchmetrics.utilities.checks import _check_same_shape
+from torchmetrics.utilities.compute import _safe_divide
+
+
+def _dice_score_validate_args(
+    num_classes: int,
+    include_background: bool,
+    average: Optional[Literal["micro", "macro", "weighted", "none"]] = "micro",
+    input_format: Literal["one-hot", "index"] = "one-hot",
+) -> None:
+    """Validate the arguments of the metric."""
+    if not isinstance(num_classes, int) or num_classes <= 0:
+        raise ValueError(f"Expected argument `num_classes` must be a positive integer, but got {num_classes}.")
+    if not isinstance(include_background, bool):
+        raise ValueError(f"Expected argument `include_background` must be a boolean, but got {include_background}.")
+    allowed_average = ["micro", "macro", "weighted", "none"]
+    if average is not None and average not in allowed_average:
+        raise ValueError(f"Expected argument `average` to be one of {allowed_average} or None, but got {average}.")
+    if input_format not in ["one-hot", "index"]:
+        raise ValueError(f"Expected argument `input_format` to be one of 'one-hot', 'index', but got {input_format}.")
+
+
+def _dice_score_update(
+    preds: Tensor,
+    target: Tensor,
+    num_classes: int,
+    include_background: bool,
+    input_format: Literal["one-hot", "index"] = "one-hot",
+) -> Tuple[Tensor, Tensor, Tensor]:
+    """Update the state with the current prediction and target."""
+    _check_same_shape(preds, target)
+    if preds.ndim < 3:
+        raise ValueError(f"Expected both `preds` and `target` to have at least 3 dimensions, but got {preds.ndim}.")
+
+    if input_format == "index":
+        preds = torch.nn.functional.one_hot(preds, num_classes=num_classes).movedim(-1, 1)
+        target = torch.nn.functional.one_hot(target, num_classes=num_classes).movedim(-1, 1)
+
+    if not include_background:
+        preds, target = _ignore_background(preds, target)
+
+    reduce_axis = list(range(2, target.ndim))
+    intersection = torch.sum(preds * target, dim=reduce_axis)
+    target_sum = torch.sum(target, dim=reduce_axis)
+    pred_sum = torch.sum(preds, dim=reduce_axis)
+
+    numerator = 2 * intersection
+    denominator = pred_sum + target_sum
+    support = target_sum
+    return numerator, denominator, support
+
+
+def _dice_score_compute(
+    numerator: Tensor,
+    denominator: Tensor,
+    average: Optional[Literal["micro", "macro", "weighted", "none"]] = "micro",
+    support: Optional[Tensor] = None,
+) -> Tensor:
+    """Compute the Dice score from the numerator and denominator."""
+    if average == "micro":
+        numerator = torch.sum(numerator, dim=-1)
+        denominator = torch.sum(denominator, dim=-1)
+    dice = _safe_divide(numerator, denominator, zero_division=1.0)
+    if average == "macro":
+        dice = torch.mean(dice, dim=-1)
+    elif average == "weighted" and support is not None:
+        weights = _safe_divide(support, torch.sum(support, dim=-1, keepdim=True), zero_division=1.0)
+        dice = torch.sum(dice * weights, dim=-1)
+    return dice
+
+
+def dice_score(
+    preds: Tensor,
+    target: Tensor,
+    num_classes: int,
+    include_background: bool = True,
+    average: Optional[Literal["micro", "macro", "weighted", "none"]] = "micro",
+    input_format: Literal["one-hot", "index"] = "one-hot",
+) -> Tensor:
+    """Compute the Dice score for semantic segmentation.
+
+    Args:
+        preds: Predictions from model
+        target: Ground truth values
+        num_classes: Number of classes
+        include_background: Whether to include the background class in the computation
+        average: The method to average the dice score. Options are ``"micro"``, ``"macro"``, ``"weighted"``, ``"none"``
+          or ``None``. This determines how to average the dice score across different classes.
+        input_format: What kind of input the function receives. Choose between ``"one-hot"`` for one-hot encoded tensors
+          or ``"index"`` for index tensors
+
+    Returns:
+        The Dice score.
+
+    Example (with one-hot encoded tensors):
+        >>> from torch import randint
+        >>> from torchmetrics.functional.segmentation import dice_score
+        >>> preds = randint(0, 2, (4, 5, 16, 16))  # 4 samples, 5 classes, 16x16 prediction
+        >>> target = randint(0, 2, (4, 5, 16, 16))  # 4 samples, 5 classes, 16x16 target
+        >>> # dice score micro averaged over all classes
+        >>> dice_score(preds, target, num_classes=5, average="micro")
+        tensor([0.4842, 0.4968, 0.5053, 0.4902])
+        >>> # dice score per sample and class
+        >>> dice_score(preds, target, num_classes=5, average="none")
+        tensor([[0.4724, 0.5185, 0.4710, 0.5062, 0.4500],
+                [0.4571, 0.4980, 0.5191, 0.4380, 0.5649],
+                [0.5428, 0.4904, 0.5358, 0.4830, 0.4724],
+                [0.4715, 0.4925, 0.4797, 0.5267, 0.4788]])
+
+    Example (with index tensors):
+        >>> from torch import randint
+        >>> from torchmetrics.functional.segmentation import dice_score
+        >>> preds = randint(0, 5, (4, 16, 16))  # 4 samples, 5 classes, 16x16 prediction
+        >>> target = randint(0, 5, (4, 16, 16))  # 4 samples, 5 classes, 16x16 target
+        >>> # dice score micro averaged over all classes
+        >>> dice_score(preds, target, num_classes=5, average="micro", input_format="index")
+        tensor([0.2031, 0.1914, 0.2500, 0.2266])
+        >>> # dice score per sample and class
+        >>> dice_score(preds, target, num_classes=5, average="none", input_format="index")
+        tensor([[0.1714, 0.2500, 0.1304, 0.2524, 0.2069],
+                [0.1837, 0.2162, 0.0962, 0.2692, 0.1895],
+                [0.3866, 0.1348, 0.2526, 0.2301, 0.2083],
+                [0.1978, 0.2804, 0.1714, 0.1915, 0.2783]])
+
+    """
+    _dice_score_validate_args(num_classes, include_background, average, input_format)
+    numerator, denominator, support = _dice_score_update(preds, target, num_classes, include_background, input_format)
+    return _dice_score_compute(numerator, denominator, average, support=support)

src/torchmetrics/functional/segmentation/generalized_dice.py

@@ -28,7 +28,7 @@ def _generalized_dice_validate_args(
     input_format: Literal["one-hot", "index"],
 ) -> None:
     """Validate the arguments of the metric."""
-    if num_classes <= 0:
+    if not isinstance(num_classes, int) or num_classes <= 0:
         raise ValueError(f"Expected argument `num_classes` must be a positive integer, but got {num_classes}.")
     if not isinstance(include_background, bool):
         raise ValueError(f"Expected argument `include_background` must be a boolean, but got {include_background}.")
@@ -116,15 +116,15 @@ def generalized_dice_score(
         target: Ground truth values
         num_classes: Number of classes
         include_background: Whether to include the background class in the computation
-        per_class: Whether to compute the IoU for each class separately, else average over all classes
+        per_class: Whether to compute the score for each class separately, else average over all classes
         weight_type: Type of weight factor to apply to the classes. One of ``"square"``, ``"simple"``, or ``"linear"``
         input_format: What kind of input the function receives. Choose between ``"one-hot"`` for one-hot encoded tensors
             or ``"index"`` for index tensors
 
     Returns:
         The Generalized Dice Score
 
-    Example:
+    Example (with one-hot encoded tensors):
         >>> from torch import randint
         >>> from torchmetrics.functional.segmentation import generalized_dice_score
         >>> preds = randint(0, 2, (4, 5, 16, 16))  # 4 samples, 5 classes, 16x16 prediction
@@ -137,6 +137,19 @@ def generalized_dice_score(
                 [0.5428, 0.4904, 0.5358, 0.4830, 0.4724],
                 [0.4715, 0.4925, 0.4797, 0.5267, 0.4788]])
 
+    Example (with index tensors):
+        >>> from torch import randint
+        >>> from torchmetrics.functional.segmentation import generalized_dice_score
+        >>> preds = randint(0, 5, (4, 16, 16))  # 4 samples, 5 classes, 16x16 prediction
+        >>> target = randint(0, 5, (4, 16, 16))  # 4 samples, 5 classes, 16x16 target
+        >>> generalized_dice_score(preds, target, num_classes=5, input_format="index")
+        tensor([0.1991, 0.1971, 0.2350, 0.2216])
+        >>> generalized_dice_score(preds, target, num_classes=5, per_class=True, input_format="index")
+        tensor([[0.1714, 0.2500, 0.1304, 0.2524, 0.2069],
+                [0.1837, 0.2162, 0.0962, 0.2692, 0.1895],
+                [0.3866, 0.1348, 0.2526, 0.2301, 0.2083],
+                [0.1978, 0.2804, 0.1714, 0.1915, 0.2783]])
+
     """
     _generalized_dice_validate_args(num_classes, include_background, per_class, weight_type, input_format)
     numerator, denominator = _generalized_dice_update(

src/torchmetrics/segmentation/__init__.py

@@ -11,8 +11,9 @@
 # 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 torchmetrics.segmentation.dice import DiceScore
 from torchmetrics.segmentation.generalized_dice import GeneralizedDiceScore
 from torchmetrics.segmentation.hausdorff_distance import HausdorffDistance
 from torchmetrics.segmentation.mean_iou import MeanIoU
 
-__all__ = ["GeneralizedDiceScore", "MeanIoU", "HausdorffDistance"]
+__all__ = ["GeneralizedDiceScore", "MeanIoU", "HausdorffDistance", "DiceScore"]