[Segmentation] Added generalized dice score metric (#1090)

* Adding generalized dice score metric
* Apply suggestions from code review

---------

Co-authored-by: Nicki Skafte Detlefsen <skaftenicki@gmail.com>
Co-authored-by: Jirka Borovec <Borda@users.noreply.github.com>
Co-authored-by: Justus Schock <12886177+justusschock@users.noreply.github.com>
Co-authored-by: Jirka <jirka.borovec@seznam.cz>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Jirka Borovec <6035284+Borda@users.noreply.github.com>

CHANGELOG.md

@@ -12,6 +12,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- Added `GeneralizedDiceScore` to segmentation package ([#1090](https://github.com/Lightning-AI/metrics/pull/1090))
+
+
 - Added `SensitivityAtSpecificity` metric to classification subpackage ([#2217](https://github.com/Lightning-AI/torchmetrics/pull/2217))
 
 
@@ -34,7 +37,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Deprecated
 
--
 
 
 ### Fixed

README.md

@@ -288,6 +288,7 @@ covers the following domains:
 - Multimodal (Image-Text)
 - Nominal
 - Regression
+- Segmentation
 - Text
 
 Each domain may require some additional dependencies which can be installed with `pip install torchmetrics[audio]`,

docs/source/index.rst

@@ -222,6 +222,14 @@ Or directly from conda
 
    retrieval/*
 
+.. toctree::
+   :maxdepth: 2
+   :name: segmentation
+   :caption: Segmentation
+   :glob:
+
+   segmentation/*
+
 .. toctree::
    :maxdepth: 2
    :name: text

docs/source/links.rst

@@ -170,3 +170,4 @@
 .. _FLORES-200: https://arxiv.org/abs/2207.04672
 .. _averaging curve objects: https://scikit-learn.org/stable/auto_examples/model_selection/plot_roc.html
 .. _SCC: https://www.ingentaconnect.com/content/tandf/tres/1998/00000019/00000004/art00013
+.. _Generalized Dice Score: https://arxiv.org/abs/1707.03237

docs/source/segmentation/generalized_dice.rst

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

src/torchmetrics/functional/classification/__init__.py

@@ -159,6 +159,7 @@
     "confusion_matrix",
     "multiclass_confusion_matrix",
     "multilabel_confusion_matrix",
+    "generalized_dice_score",
     "dice",
     "exact_match",
     "multiclass_exact_match",

src/torchmetrics/functional/segmentation/__init__.py

@@ -11,3 +11,7 @@
 # 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.generalized_dice import generalized_dice_score
+
+__all__ = ["generalized_dice_score"]

src/torchmetrics/functional/segmentation/generalized_dice.py

@@ -0,0 +1,138 @@
+# 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.
+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 _generalized_dice_validate_args(
+    num_classes: int,
+    include_background: bool,
+    per_class: bool,
+    weight_type: Literal["square", "simple", "linear"],
+) -> None:
+    """Validate the arguments of the metric."""
+    if 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}.")
+    if not isinstance(per_class, bool):
+        raise ValueError(f"Expected argument `per_class` must be a boolean, but got {per_class}.")
+    if weight_type not in ["square", "simple", "linear"]:
+        raise ValueError(
+            f"Expected argument `weight_type` to be one of 'square', 'simple', 'linear', but got {weight_type}."
+        )
+
+
+def _generalized_dice_update(
+    preds: Tensor,
+    target: Tensor,
+    num_classes: int,
+    include_background: bool,
+    weight_type: Literal["square", "simple", "linear"] = "square",
+) -> 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 (preds.bool() != preds).any():  # preds is an index tensor
+        preds = torch.nn.functional.one_hot(preds, num_classes=num_classes).movedim(-1, 1)
+    if (target.bool() != target).any():  # target is an index tensor
+        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)
+    cardinality = target_sum + pred_sum
+
+    if weight_type == "simple":
+        weights = 1.0 / target_sum
+    elif weight_type == "linear":
+        weights = torch.ones_like(target_sum)
+    elif weight_type == "square":
+        weights = 1.0 / (target_sum**2)
+    else:
+        raise ValueError(
+            f"Expected argument `weight_type` to be one of 'simple', 'linear', 'square', but got {weight_type}."
+        )
+
+    w_shape = weights.shape
+    weights_flatten = weights.flatten()
+    infs = torch.isinf(weights_flatten)
+    weights_flatten[infs] = 0
+    w_max = torch.max(weights, 0).values.repeat(w_shape[0], 1).T.flatten()
+    weights_flatten[infs] = w_max[infs]
+    weights = weights_flatten.reshape(w_shape)
+
+    numerator = 2.0 * intersection * weights
+    denominator = cardinality * weights
+    return numerator, denominator  # type:ignore[return-value]
+
+
+def _generalized_dice_compute(numerator: Tensor, denominator: Tensor, per_class: bool = True) -> Tensor:
+    """Compute the generalized dice score."""
+    if not per_class:
+        numerator = torch.sum(numerator, 1)
+        denominator = torch.sum(denominator, 1)
+    return _safe_divide(numerator, denominator)
+
+
+def generalized_dice_score(
+    preds: Tensor,
+    target: Tensor,
+    num_classes: int,
+    include_background: bool = True,
+    per_class: bool = False,
+    weight_type: Literal["square", "simple", "linear"] = "square",
+) -> Tensor:
+    """Compute the Generalized 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
+        per_class: Whether to compute the IoU 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"``
+
+    Returns:
+        The Generalized Dice Score
+
+    Example:
+        >>> import torch
+        >>> _ = torch.manual_seed(42)
+        >>> from torchmetrics.functional.segmentation import generalized_dice_score
+        >>> preds = torch.randint(0, 2, (4, 5, 16, 16))  # 4 samples, 5 classes, 16x16 prediction
+        >>> target = torch.randint(0, 2, (4, 5, 16, 16))  # 4 samples, 5 classes, 16x16 target
+        >>> generalized_dice_score(preds, target, num_classes=5)
+        tensor([0.4830, 0.4935, 0.5044, 0.4880])
+        >>> generalized_dice_score(preds, target, num_classes=5, per_class=True)
+        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]])
+
+    """
+    _generalized_dice_validate_args(num_classes, include_background, per_class, weight_type)
+    numerator, denominator = _generalized_dice_update(preds, target, num_classes, include_background, weight_type)
+    return _generalized_dice_compute(numerator, denominator, per_class)

src/torchmetrics/functional/segmentation/utils.py

@@ -24,6 +24,13 @@
 from torchmetrics.utilities.imports import _SCIPY_AVAILABLE
 
 
+def _ignore_background(preds: Tensor, target: Tensor) -> Tuple[Tensor, Tensor]:
+    """Ignore the background class in the computation."""
+    preds = preds[:, 1:] if preds.shape[1] > 1 else preds
+    target = target[:, 1:] if target.shape[1] > 1 else target
+    return preds, target
+
+
 def check_if_binarized(x: Tensor) -> None:
     """Check if the input is binarized.
 

src/torchmetrics/segmentation/__init__.py

@@ -0,0 +1,17 @@
+# 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 torchmetrics.segmentation.generalized_dice import GeneralizedDiceScore
+
+__all__ = ["GeneralizedDiceScore"]