tversky.py

# 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 warnings
from collections.abc import Callable

import torch
from torch.nn.modules.loss import _Loss

from monai.losses.utils import compute_tp_fp_fn
from monai.metrics.utils import create_ignore_mask
from monai.networks import one_hot
from monai.utils import LossReduction


class TverskyLoss(_Loss):
    """
    Compute the Tversky loss defined in:

        Sadegh et al. (2017) Tversky loss function for image segmentation
        using 3D fully convolutional deep networks. (https://arxiv.org/abs/1706.05721)

        Wang, Z. et. al. (2023) Dice Semimetric Losses: Optimizing the Dice Score with
        Soft Labels. MICCAI 2023.

    Adapted from:
        https://github.com/NifTK/NiftyNet/blob/v0.6.0/niftynet/layer/loss_segmentation.py#L631

    """

    def __init__(
        self,
        include_background: bool = True,
        to_onehot_y: bool = False,
        sigmoid: bool = False,
        softmax: bool = False,
        other_act: Callable | None = None,
        alpha: float = 0.5,
        beta: float = 0.5,
        reduction: LossReduction | str = LossReduction.MEAN,
        smooth_nr: float = 1e-5,
        smooth_dr: float = 1e-5,
        batch: bool = False,
        soft_label: bool = False,
        ignore_index: int | None = None,
    ) -> None:
        """
        Args:
            include_background: If False channel index 0 (background category) is excluded from the calculation.
            to_onehot_y: whether to convert `y` into the one-hot format. Defaults to False.
            sigmoid: If True, apply a sigmoid function to the prediction.
            softmax: If True, apply a softmax function to the prediction.
            other_act: if don't want to use `sigmoid` or `softmax`, use other callable function to execute
                other activation layers, Defaults to ``None``. for example:
                `other_act = torch.tanh`.
            alpha: weight of false positives
            beta: weight of false negatives
            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.

            smooth_nr: a small constant added to the numerator to avoid zero.
            smooth_dr: a small constant added to the denominator to avoid nan.
            batch: whether to sum the intersection and union areas over the batch dimension before the dividing.
                Defaults to False, a Dice loss value is computed independently from each item in the batch
                before any `reduction`.
            soft_label: whether the target contains non-binary values (soft labels) or not.
                If True a soft label formulation of the loss will be used.
            ignore_index: index of the class to ignore during calculation.

        Raises:
            TypeError: When ``other_act`` is not an ``Optional[Callable]``.
            ValueError: When more than 1 of [``sigmoid=True``, ``softmax=True``, ``other_act is not None``].
                Incompatible values.

        """

        super().__init__(reduction=LossReduction(reduction).value)
        if other_act is not None and not callable(other_act):
            raise TypeError(f"other_act must be None or callable but is {type(other_act).__name__}.")
        if int(sigmoid) + int(softmax) + int(other_act is not None) > 1:
            raise ValueError("Incompatible values: more than 1 of [sigmoid=True, softmax=True, other_act is not None].")
        self.include_background = include_background
        self.to_onehot_y = to_onehot_y
        self.sigmoid = sigmoid
        self.softmax = softmax
        self.other_act = other_act
        self.alpha = alpha
        self.beta = beta
        self.smooth_nr = float(smooth_nr)
        self.smooth_dr = float(smooth_dr)
        self.batch = batch
        self.soft_label = soft_label
        self.ignore_index = ignore_index

    def forward(self, input: torch.Tensor, target: torch.Tensor) -> torch.Tensor:
        """
        Args:
            input: the shape should be BNH[WD].
            target: the shape should be BNH[WD].

        Raises:
            ValueError: When ``self.reduction`` is not one of ["mean", "sum", "none"].

        """
        if self.sigmoid:
            input = torch.sigmoid(input)

        n_pred_ch = input.shape[1]
        if self.softmax:
            if n_pred_ch == 1:
                warnings.warn("single channel prediction, `softmax=True` ignored.")
            else:
                input = torch.softmax(input, 1)

        if self.other_act is not None:
            input = self.other_act(input)

        if self.to_onehot_y:
            if n_pred_ch == 1:
                warnings.warn("single channel prediction, `to_onehot_y=True` ignored.")
            else:
                original_target = target
                target = one_hot(target, num_classes=n_pred_ch)

        if self.ignore_index is not None:
            mask_src = original_target if self.to_onehot_y and n_pred_ch > 1 else target
            mask = create_ignore_mask(mask_src, self.ignore_index)
            if mask is not None:
                input = input * mask
                target = target * mask

        if not self.include_background:
            if n_pred_ch == 1:
                warnings.warn("single channel prediction, `include_background=False` ignored.")
            else:
                # if skipping background, removing first channel
                target = target[:, 1:]
                input = input[:, 1:]

        if target.shape != input.shape:
            raise AssertionError(f"ground truth has differing shape ({target.shape}) from input ({input.shape})")

        # reducing only spatial dimensions (not batch nor channels)
        reduce_axis: list[int] = torch.arange(2, len(input.shape)).tolist()
        if self.batch:
            # reducing spatial dimensions and batch
            reduce_axis = [0] + reduce_axis

        tp, fp, fn = compute_tp_fp_fn(input, target, reduce_axis, 1, self.soft_label, False)
        fp *= self.alpha
        fn *= self.beta
        numerator = tp + self.smooth_nr
        denominator = tp + fp + fn + self.smooth_dr

        score: torch.Tensor = 1.0 - numerator / denominator

        if self.reduction == LossReduction.SUM.value:
            return torch.sum(score)  # sum over the batch and channel dims
        if self.reduction == LossReduction.NONE.value:
            return score  # returns [N, num_classes] losses
        if self.reduction == LossReduction.MEAN.value:
            return torch.mean(score)
        raise ValueError(f'Unsupported reduction: {self.reduction}, available options are ["mean", "sum", "none"].')