deepreg.loss.label.JaccardIndex.get_config() - Code Metrics - Inspection of "734 large dice" - DeepRegNet/DeepReg - Measure and Improve Code Quality continuously with Scrutinizer

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Pull Request — main (#736)

by Yunguan

created 2021-04-04 01:24 UTC

deepreg.loss.label.JaccardIndex.get_config() A

↳ Parent: deepreg.loss.label

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Total Lines	5
Code Lines	4

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eloc	4
dl	0
loc	5
rs	10
c	0
b	0
f	0
cc	1
nop	1

"""Provide different loss or metrics classes for labels."""

from typing import List, Optional

import tensorflow as tf

from deepreg.constant import EPS
from deepreg.loss.util import NegativeLossMixin, cauchy_kernel1d
from deepreg.loss.util import gaussian_kernel1d_sigma as gaussian_kernel1d
from deepreg.loss.util import separable_filter
from deepreg.registry import REGISTRY


class MultiScaleLoss(tf.keras.losses.Loss):
    """
    Base class for multi-scale loss.

    It applies the loss at different scales (gaussian or cauchy smoothing).
    It is assumed that loss values are between 0 and 1.
    """

    kernel_fn_dict = dict(gaussian=gaussian_kernel1d, cauchy=cauchy_kernel1d)

    def __init__(
        self,
        scales: Optional[List] = None,
        kernel: str = "gaussian",
        reduction: str = tf.keras.losses.Reduction.NONE,
        name: str = "MultiScaleLoss",
    ):
        """
        Init.

        :param scales: list of scalars or None, if None, do not apply any scaling.
        :param kernel: gaussian or cauchy.
        :param reduction: using SUM reduction over batch axis,
            this is for supporting multi-device training,
            and the loss will be divided by global batch size,
            calling the loss like `loss(y_true, y_pred)` will return a scalar tensor.
        :param name: str, name of the loss.
        """
        super().__init__(reduction=reduction, name=name)
        assert kernel in ["gaussian", "cauchy"]
        self.scales = scales
        self.kernel = kernel

    def call(self, y_true: tf.Tensor, y_pred: tf.Tensor) -> tf.Tensor:
        """
        Use _call to calculate loss at different scales.

        :param y_true: ground-truth tensor, shape = (batch, dim1, dim2, dim3).
        :param y_pred: predicted tensor, shape = (batch, dim1, dim2, dim3).
        :return: multi-scale loss, shape = (batch, ).
        """
        if self.scales is None:
            return self._call(y_true=y_true, y_pred=y_pred)
        kernel_fn = self.kernel_fn_dict[self.kernel]
        losses = []
        for s in self.scales:
            if s == 0:
                # no smoothing
                losses.append(
                    self._call(
                        y_true=y_true,
                        y_pred=y_pred,
                    )
                )
            else:
                losses.append(
                    self._call(
                        y_true=separable_filter(
                            tf.expand_dims(y_true, axis=4), kernel_fn(s)
                        )[..., 0],
                        y_pred=separable_filter(
                            tf.expand_dims(y_pred, axis=4), kernel_fn(s)
                        )[..., 0],
                    )
                )
        loss = tf.add_n(losses)
        loss = loss / len(self.scales)
        return loss

    def _call(self, y_true: tf.Tensor, y_pred: tf.Tensor) -> tf.Tensor:
        """
        Return loss for a batch.

        :param y_true: ground-truth tensor.
        :param y_pred: predicted tensor.
        :return: negated loss.
        """
        raise NotImplementedError

    def get_config(self) -> dict:
        """Return the config dictionary for recreating this class."""
        config = super().get_config()
        config["scales"] = self.scales
        config["kernel"] = self.kernel
        return config


class DiceScore(MultiScaleLoss):
    """
    Define dice score.

    The formulation is:

        0. w_fg + w_bg = 1
        1. let y_prod = y_true * y_pred and y_sum  = y_true + y_pred
        2. num = 2 *  (w_fg * y_true * y_pred + w_bg * (1−y_true) * (1−y_pred))
               = 2 *  ((w_fg+w_bg) * y_prod - w_bg * y_sum + w_bg)
               = 2 *  (y_prod - w_bg * y_sum + w_bg)
        3. denom = (w_fg * (y_true + y_pred) + w_bg * (1−y_true + 1−y_pred))
                 = (w_fg-w_bg) * y_sum + 2 * w_bg
                 = (1-2*w_bg) * y_sum + 2 * w_bg
        4. dice score = num / denom

    where num and denom are summed over all axes except the batch axis.

    Reference:
        Sudre, Carole H., et al. "Generalised dice overlap as a deep learning loss
        function for highly unbalanced segmentations." Deep learning in medical image
        analysis and multimodal learning for clinical decision support.
        Springer, Cham, 2017. 240-248.
    """

    def __init__(
        self,
        binary: bool = False,
        background_weight: float = 0.0,
        smooth_nr: float = EPS,
        smooth_dr: float = EPS,
        scales: Optional[List] = None,
        kernel: str = "gaussian",
        reduction: str = tf.keras.losses.Reduction.NONE,
        name: str = "DiceScore",
    ):
        """
        Init.

        :param binary: if True, project y_true, y_pred to 0 or 1.
        :param background_weight: weight for background, where y == 0.
        :param smooth_nr: small constant added to numerator in case of zero covariance.
        :param smooth_dr: small constant added to denominator in case of zero variance.
        :param scales: list of scalars or None, if None, do not apply any scaling.
        :param kernel: gaussian or cauchy.
        :param reduction: using SUM reduction over batch axis,
            this is for supporting multi-device training,
            and the loss will be divided by global batch size,
            calling the loss like `loss(y_true, y_pred)` will return a scalar tensor.
        :param name: str, name of the loss.
        """
        super().__init__(scales=scales, kernel=kernel, reduction=reduction, name=name)
        if background_weight < 0 or background_weight > 1:
            raise ValueError(
                "The background weight for Dice Score must be "
                f"within [0, 1], got {background_weight}."
            )

        self.binary = binary
        self.background_weight = background_weight
        self.smooth_nr = smooth_nr
        self.smooth_dr = smooth_dr
        self.flatten = tf.keras.layers.Flatten()

    def _call(self, y_true: tf.Tensor, y_pred: tf.Tensor) -> tf.Tensor:
        """
        Return loss for a batch.

        :param y_true: shape = (batch, ...)
        :param y_pred: shape = (batch, ...)
        :return: shape = (batch,)
        """
        if self.binary:
            y_true = tf.cast(y_true >= 0.5, dtype=y_true.dtype)
            y_pred = tf.cast(y_pred >= 0.5, dtype=y_pred.dtype)

        # (batch, ...) -> (batch, d)
        y_true = self.flatten(y_true)
        y_pred = self.flatten(y_pred)

        # for foreground class
        y_prod = tf.reduce_sum(y_true * y_pred, axis=1)
        y_sum = tf.reduce_sum(y_true + y_pred, axis=1)

        if self.background_weight > 0:
            # generalized
            vol = tf.reduce_sum(tf.ones_like(y_true), axis=1)
            numerator = 2 * (
                y_prod - self.background_weight * y_sum + self.background_weight * vol
            )
            denominator = (
                1 - 2 * self.background_weight
            ) * y_sum + 2 * self.background_weight * vol
        else:
            # foreground only
            numerator = 2 * y_prod
            denominator = y_sum

        return (numerator + self.smooth_nr) / (denominator + self.smooth_dr)

    def get_config(self) -> dict:
        """Return the config dictionary for recreating this class."""
        config = super().get_config()
        config.update(
            binary=self.binary,
            background_weight=self.background_weight,
            smooth_nr=self.smooth_nr,
            smooth_dr=self.smooth_dr,
        )
        return config


@REGISTRY.register_loss(name="dice")
class DiceLoss(NegativeLossMixin, DiceScore):
    """Revert the sign of DiceScore."""


@REGISTRY.register_loss(name="cross-entropy")
class CrossEntropy(MultiScaleLoss):
    """
    Define weighted cross-entropy.

    The formulation is:
        loss = − w_fg * y_true log(y_pred) - w_bg * (1−y_true) log(1−y_pred)
    """

    def __init__(
        self,
        binary: bool = False,
        background_weight: float = 0.0,
        smooth: float = EPS,
        scales: Optional[List] = None,
        kernel: str = "gaussian",
        reduction: str = tf.keras.losses.Reduction.NONE,
        name: str = "CrossEntropy",
    ):
        """
        Init.

        :param binary: if True, project y_true, y_pred to 0 or 1
        :param background_weight: weight for background, where y == 0.
        :param scales: list of scalars or None, if None, do not apply any scaling.
        :param kernel: gaussian or cauchy.
        :param reduction: using SUM reduction over batch axis,
            this is for supporting multi-device training,
            and the loss will be divided by global batch size,
            calling the loss like `loss(y_true, y_pred)` will return a scalar tensor.
        :param name: str, name of the loss.
        """
        super().__init__(scales=scales, kernel=kernel, reduction=reduction, name=name)
        if background_weight < 0 or background_weight > 1:
            raise ValueError(
                "The background weight for Cross Entropy must be "
                f"within [0, 1], got {background_weight}."
            )
        self.binary = binary
        self.background_weight = background_weight
        self.smooth = smooth
        self.flatten = tf.keras.layers.Flatten()

    def _call(self, y_true: tf.Tensor, y_pred: tf.Tensor) -> tf.Tensor:
        """
        Return loss for a batch.

        :param y_true: shape = (batch, ...)
        :param y_pred: shape = (batch, ...)
        :return: shape = (batch,)
        """
        if self.binary:
            y_true = tf.cast(y_true >= 0.5, dtype=y_true.dtype)
            y_pred = tf.cast(y_pred >= 0.5, dtype=y_pred.dtype)

        # (batch, ...) -> (batch, d)
        y_true = self.flatten(y_true)
        y_pred = self.flatten(y_pred)

        loss_fg = -tf.reduce_mean(y_true * tf.math.log(y_pred + self.smooth), axis=1)
        if self.background_weight > 0:
            loss_bg = -tf.reduce_mean(
                (1 - y_true) * tf.math.log(1 - y_pred + self.smooth), axis=1
            )
            return (
                1 - self.background_weight
            ) * loss_fg + self.background_weight * loss_bg
        else:
            return loss_fg

    def get_config(self) -> dict:
        """Return the config dictionary for recreating this class."""
        config = super().get_config()
        config.update(
            binary=self.binary,
            background_weight=self.background_weight,
            smooth=self.smooth,
        )
        return config


class JaccardIndex(DiceScore):
    """
    Define Jaccard index.

    The formulation is:
    1. num = y_true * y_pred
    2. denom = y_true + y_pred - y_true * y_pred
    3. Jaccard index = num / denom

        0. w_fg + w_bg = 1
        1. let y_prod = y_true * y_pred and y_sum  = y_true + y_pred
        2. num = (w_fg * y_true * y_pred + w_bg * (1−y_true) * (1−y_pred))
               = ((w_fg+w_bg) * y_prod - w_bg * y_sum + w_bg)
               = (y_prod - w_bg * y_sum + w_bg)
        3. denom = (w_fg * (y_true + y_pred - y_true * y_pred)
                  + w_bg * (1−y_true + 1−y_pred - (1−y_true) * (1−y_pred)))
                 = w_fg * (y_sum - y_prod) + w_bg * (1-y_prod)
                 = (1-w_bg) * y_sum - y_prod + w_bg
        4. dice score = num / denom
    """

    def __init__(
        self,
        binary: bool = False,
        background_weight: float = 0.0,
        smooth_nr: float = EPS,
        smooth_dr: float = EPS,
        scales: Optional[List] = None,
        kernel: str = "gaussian",
        reduction: str = tf.keras.losses.Reduction.NONE,
        name: str = "JaccardIndex",
    ):
        """
        Init.

        :param binary: if True, project y_true, y_pred to 0 or 1.
        :param background_weight: weight for background, where y == 0.
        :param smooth_nr: small constant added to numerator in case of zero covariance.
        :param smooth_dr: small constant added to denominator in case of zero variance.
        :param scales: list of scalars or None, if None, do not apply any scaling.
        :param kernel: gaussian or cauchy.
        :param reduction: using SUM reduction over batch axis,
            this is for supporting multi-device training,
            and the loss will be divided by global batch size,
            calling the loss like `loss(y_true, y_pred)` will return a scalar tensor.
        :param name: str, name of the loss.
        """
        super().__init__(
            binary=binary,
            background_weight=background_weight,
            smooth_nr=smooth_nr,
            smooth_dr=smooth_dr,
            scales=scales,
            kernel=kernel,
            reduction=reduction,
            name=name,
        )

    def _call(self, y_true: tf.Tensor, y_pred: tf.Tensor) -> tf.Tensor:
        """
        Return loss for a batch.

        :param y_true: shape = (batch, ...)
        :param y_pred: shape = (batch, ...)
        :return: shape = (batch,)
        """
        if self.binary:
            y_true = tf.cast(y_true >= 0.5, dtype=y_true.dtype)
            y_pred = tf.cast(y_pred >= 0.5, dtype=y_pred.dtype)

        # (batch, ...) -> (batch, d)
        y_true = self.flatten(y_true)
        y_pred = self.flatten(y_pred)

        # for foreground class
        y_prod = tf.reduce_sum(y_true * y_pred, axis=1)
        y_sum = tf.reduce_sum(y_true + y_pred, axis=1)

        if self.background_weight > 0:
            # generalized
            vol = tf.reduce_sum(tf.ones_like(y_true), axis=1)
            numerator = (
                y_prod - self.background_weight * y_sum + self.background_weight * vol
            )
            denominator = (
                (1 - self.background_weight) * y_sum
                - y_prod
                + self.background_weight * vol
            )
        else:
            # foreground only
            numerator = y_prod
            denominator = y_sum - y_prod

        return (numerator + self.smooth_nr) / (denominator + self.smooth_dr)


@REGISTRY.register_loss(name="jaccard")
class JaccardLoss(NegativeLossMixin, JaccardIndex):
    """Revert the sign of JaccardIndex."""


def compute_centroid(mask: tf.Tensor, grid: tf.Tensor) -> tf.Tensor:
    """
    Calculate the centroid of the mask.
    :param mask: shape = (batch, dim1, dim2, dim3)
    :param grid: shape = (1, dim1, dim2, dim3, 3)
    :return: shape = (batch, 3), batch of vectors denoting
             location of centroids.
    """
    assert len(mask.shape) == 4
    assert len(grid.shape) == 5
    bool_mask = tf.expand_dims(
        tf.cast(mask >= 0.5, dtype=tf.float32), axis=4
    )  # (batch, dim1, dim2, dim3, 1)
    masked_grid = bool_mask * grid  # (batch, dim1, dim2, dim3, 3)
    numerator = tf.reduce_sum(masked_grid, axis=[1, 2, 3])  # (batch, 3)
    denominator = tf.reduce_sum(bool_mask, axis=[1, 2, 3])  # (batch, 1)
    return (numerator + EPS) / (denominator + EPS)  # (batch, 3)


def compute_centroid_distance(
    y_true: tf.Tensor, y_pred: tf.Tensor, grid: tf.Tensor
) -> tf.Tensor:
    """
    Calculate the L2-distance between two tensors' centroids.
    :param y_true: tensor, shape = (batch, dim1, dim2, dim3)
    :param y_pred: tensor, shape = (batch, dim1, dim2, dim3)
    :param grid: tensor, shape = (1, dim1, dim2, dim3, 3)
    :return: shape = (batch,)
    """
    centroid_1 = compute_centroid(mask=y_pred, grid=grid)  # (batch, 3)
    centroid_2 = compute_centroid(mask=y_true, grid=grid)  # (batch, 3)
    return tf.sqrt(tf.reduce_sum((centroid_1 - centroid_2) ** 2, axis=1))


def foreground_proportion(y: tf.Tensor) -> tf.Tensor:
    """
    Calculate the percentage of foreground vs background per 3d volume.
    :param y: shape = (batch, dim1, dim2, dim3), a 3D label tensor
    :return: shape = (batch,)
    """
    y = tf.cast(y >= 0.5, dtype=tf.float32)
    return tf.reduce_sum(y, axis=[1, 2, 3]) / tf.reduce_sum(
        tf.ones_like(y), axis=[1, 2, 3]
    )


1			"""Provide different loss or metrics classes for labels."""
2
3			from typing import List, Optional
4
5			import tensorflow as tf
6
7			from deepreg.constant import EPS
8			from deepreg.loss.util import NegativeLossMixin, cauchy_kernel1d
9			from deepreg.loss.util import gaussian_kernel1d_sigma as gaussian_kernel1d
10			from deepreg.loss.util import separable_filter
11			from deepreg.registry import REGISTRY
12
13
14			class MultiScaleLoss(tf.keras.losses.Loss):
15			"""
16			Base class for multi-scale loss.
17
18			It applies the loss at different scales (gaussian or cauchy smoothing).
19			It is assumed that loss values are between 0 and 1.
20			"""
21
22			kernel_fn_dict = dict(gaussian=gaussian_kernel1d, cauchy=cauchy_kernel1d)
23
24			def __init__(
25			self,
26			scales: Optional[List] = None,
27			kernel: str = "gaussian",
28			reduction: str = tf.keras.losses.Reduction.NONE,
29			name: str = "MultiScaleLoss",
30			):
31			"""
32			Init.
33
34			:param scales: list of scalars or None, if None, do not apply any scaling.
35			:param kernel: gaussian or cauchy.
36			:param reduction: using SUM reduction over batch axis,
37			this is for supporting multi-device training,
38			and the loss will be divided by global batch size,
39			calling the loss like `loss(y_true, y_pred)` will return a scalar tensor.
40			:param name: str, name of the loss.
41			"""
42			super().__init__(reduction=reduction, name=name)
43			assert kernel in ["gaussian", "cauchy"]
44			self.scales = scales
45			self.kernel = kernel
46
47			def call(self, y_true: tf.Tensor, y_pred: tf.Tensor) -> tf.Tensor:
48			"""
49			Use _call to calculate loss at different scales.
50
51			:param y_true: ground-truth tensor, shape = (batch, dim1, dim2, dim3).
52			:param y_pred: predicted tensor, shape = (batch, dim1, dim2, dim3).
53			:return: multi-scale loss, shape = (batch, ).
54			"""
55			if self.scales is None:
56			return self._call(y_true=y_true, y_pred=y_pred)
57			kernel_fn = self.kernel_fn_dict[self.kernel]
58			losses = []
59			for s in self.scales:
60			if s == 0:
61			# no smoothing
62			losses.append(
63			self._call(
64			y_true=y_true,
65			y_pred=y_pred,
66			)
67			)
68			else:
69			losses.append(
70			self._call(
71			y_true=separable_filter(
72			tf.expand_dims(y_true, axis=4), kernel_fn(s)
73			)[..., 0],
74			y_pred=separable_filter(
75			tf.expand_dims(y_pred, axis=4), kernel_fn(s)
76			)[..., 0],
77			)
78			)
79			loss = tf.add_n(losses)
80			loss = loss / len(self.scales)
81			return loss
82
83			def _call(self, y_true: tf.Tensor, y_pred: tf.Tensor) -> tf.Tensor:
84			"""
85			Return loss for a batch.
86
87			:param y_true: ground-truth tensor.
88			:param y_pred: predicted tensor.
89			:return: negated loss.
90			"""
91			raise NotImplementedError
92
93			def get_config(self) -> dict:
94			"""Return the config dictionary for recreating this class."""
95			config = super().get_config()
96			config["scales"] = self.scales
97			config["kernel"] = self.kernel
98			return config
99
100
101			class DiceScore(MultiScaleLoss):
102			"""
103			Define dice score.
104
105			The formulation is:
106
107			0. w_fg + w_bg = 1
108			1. let y_prod = y_true * y_pred and y_sum = y_true + y_pred
109			2. num = 2 * (w_fg * y_true * y_pred + w_bg * (1−y_true) * (1−y_pred))
110			= 2 * ((w_fg+w_bg) * y_prod - w_bg * y_sum + w_bg)
111			= 2 * (y_prod - w_bg * y_sum + w_bg)
112			3. denom = (w_fg * (y_true + y_pred) + w_bg * (1−y_true + 1−y_pred))
113			= (w_fg-w_bg) * y_sum + 2 * w_bg
114			= (1-2w_bg) y_sum + 2 * w_bg
115			4. dice score = num / denom
116
117			where num and denom are summed over all axes except the batch axis.
118
119			Reference:
120			Sudre, Carole H., et al. "Generalised dice overlap as a deep learning loss
121			function for highly unbalanced segmentations." Deep learning in medical image
122			analysis and multimodal learning for clinical decision support.
123			Springer, Cham, 2017. 240-248.
124			"""
125
126			def __init__(
127			self,
128			binary: bool = False,
129			background_weight: float = 0.0,
130			smooth_nr: float = EPS,
131			smooth_dr: float = EPS,
132			scales: Optional[List] = None,
133			kernel: str = "gaussian",
134			reduction: str = tf.keras.losses.Reduction.NONE,
135			name: str = "DiceScore",
136			):
137			"""
138			Init.
139
140			:param binary: if True, project y_true, y_pred to 0 or 1.
141			:param background_weight: weight for background, where y == 0.
142			:param smooth_nr: small constant added to numerator in case of zero covariance.
143			:param smooth_dr: small constant added to denominator in case of zero variance.
144			:param scales: list of scalars or None, if None, do not apply any scaling.
145			:param kernel: gaussian or cauchy.
146			:param reduction: using SUM reduction over batch axis,
147			this is for supporting multi-device training,
148			and the loss will be divided by global batch size,
149			calling the loss like `loss(y_true, y_pred)` will return a scalar tensor.
150			:param name: str, name of the loss.
151			"""
152			super().__init__(scales=scales, kernel=kernel, reduction=reduction, name=name)
153			if background_weight < 0 or background_weight > 1:
154			raise ValueError(
155			"The background weight for Dice Score must be "
156			f"within [0, 1], got {background_weight}."
157			)
158
159			self.binary = binary
160			self.background_weight = background_weight
161			self.smooth_nr = smooth_nr
162			self.smooth_dr = smooth_dr
163			self.flatten = tf.keras.layers.Flatten()
164
165			def _call(self, y_true: tf.Tensor, y_pred: tf.Tensor) -> tf.Tensor:
166			"""
167			Return loss for a batch.
168
169			:param y_true: shape = (batch, ...)
170			:param y_pred: shape = (batch, ...)
171			:return: shape = (batch,)
172			"""
173			if self.binary:
174			y_true = tf.cast(y_true >= 0.5, dtype=y_true.dtype)
175			y_pred = tf.cast(y_pred >= 0.5, dtype=y_pred.dtype)
176
177			# (batch, ...) -> (batch, d)
178			y_true = self.flatten(y_true)
179			y_pred = self.flatten(y_pred)
180
181			# for foreground class
182			y_prod = tf.reduce_sum(y_true * y_pred, axis=1)
183			y_sum = tf.reduce_sum(y_true + y_pred, axis=1)
184
185			if self.background_weight > 0:
186			# generalized
187			vol = tf.reduce_sum(tf.ones_like(y_true), axis=1)
188			numerator = 2 * (
189			y_prod - self.background_weight * y_sum + self.background_weight * vol
190			)
191			denominator = (
192			1 - 2 * self.background_weight
193			) * y_sum + 2 * self.background_weight * vol
194			else:
195			# foreground only
196			numerator = 2 * y_prod
197			denominator = y_sum
198
199			return (numerator + self.smooth_nr) / (denominator + self.smooth_dr)
200
201			def get_config(self) -> dict:
202			"""Return the config dictionary for recreating this class."""
203			config = super().get_config()
204			config.update(
205			binary=self.binary,
206			background_weight=self.background_weight,
207			smooth_nr=self.smooth_nr,
208			smooth_dr=self.smooth_dr,
209			)
210			return config
211
212
213			@REGISTRY.register_loss(name="dice")
214			class DiceLoss(NegativeLossMixin, DiceScore):
215			"""Revert the sign of DiceScore."""
216
217
218			@REGISTRY.register_loss(name="cross-entropy")
219			class CrossEntropy(MultiScaleLoss):
220			"""
221			Define weighted cross-entropy.
222
223			The formulation is:
224			loss = − w_fg * y_true log(y_pred) - w_bg * (1−y_true) log(1−y_pred)
225			"""
226
227			def __init__(
228			self,
229			binary: bool = False,
230			background_weight: float = 0.0,
231			smooth: float = EPS,
232			scales: Optional[List] = None,
233			kernel: str = "gaussian",
234			reduction: str = tf.keras.losses.Reduction.NONE,
235			name: str = "CrossEntropy",
236			):
237			"""
238			Init.
239
240			:param binary: if True, project y_true, y_pred to 0 or 1
241			:param background_weight: weight for background, where y == 0.
242			:param scales: list of scalars or None, if None, do not apply any scaling.
243			:param kernel: gaussian or cauchy.
244			:param reduction: using SUM reduction over batch axis,
245			this is for supporting multi-device training,
246			and the loss will be divided by global batch size,
247			calling the loss like `loss(y_true, y_pred)` will return a scalar tensor.
248			:param name: str, name of the loss.
249			"""
250			super().__init__(scales=scales, kernel=kernel, reduction=reduction, name=name)
251			if background_weight < 0 or background_weight > 1:
252			raise ValueError(
253			"The background weight for Cross Entropy must be "
254			f"within [0, 1], got {background_weight}."
255			)
256			self.binary = binary
257			self.background_weight = background_weight
258			self.smooth = smooth
259			self.flatten = tf.keras.layers.Flatten()
260
261			def _call(self, y_true: tf.Tensor, y_pred: tf.Tensor) -> tf.Tensor:
262			"""
263			Return loss for a batch.
264
265			:param y_true: shape = (batch, ...)
266			:param y_pred: shape = (batch, ...)
267			:return: shape = (batch,)
268			"""
269			if self.binary:
270			y_true = tf.cast(y_true >= 0.5, dtype=y_true.dtype)
271			y_pred = tf.cast(y_pred >= 0.5, dtype=y_pred.dtype)
272
273			# (batch, ...) -> (batch, d)
274			y_true = self.flatten(y_true)
275			y_pred = self.flatten(y_pred)
276
277			loss_fg = -tf.reduce_mean(y_true * tf.math.log(y_pred + self.smooth), axis=1)
278			if self.background_weight > 0:
279			loss_bg = -tf.reduce_mean(
280			(1 - y_true) * tf.math.log(1 - y_pred + self.smooth), axis=1
281			)
282			return (
283			1 - self.background_weight
284			) * loss_fg + self.background_weight * loss_bg
285			else:
286			return loss_fg
287
288			def get_config(self) -> dict:
289			"""Return the config dictionary for recreating this class."""
290			config = super().get_config()
291			config.update(
292			binary=self.binary,
293			background_weight=self.background_weight,
294			smooth=self.smooth,
295			)
296			return config
297
298
299			class JaccardIndex(DiceScore):
300			"""
301			Define Jaccard index.
302
303			The formulation is:
304			1. num = y_true * y_pred
305			2. denom = y_true + y_pred - y_true * y_pred
306			3. Jaccard index = num / denom
307
308			0. w_fg + w_bg = 1
309			1. let y_prod = y_true * y_pred and y_sum = y_true + y_pred
310			2. num = (w_fg * y_true * y_pred + w_bg * (1−y_true) * (1−y_pred))
311			= ((w_fg+w_bg) * y_prod - w_bg * y_sum + w_bg)
312			= (y_prod - w_bg * y_sum + w_bg)
313			3. denom = (w_fg * (y_true + y_pred - y_true * y_pred)
314			+ w_bg * (1−y_true + 1−y_pred - (1−y_true) * (1−y_pred)))
315			= w_fg * (y_sum - y_prod) + w_bg * (1-y_prod)
316			= (1-w_bg) * y_sum - y_prod + w_bg
317			4. dice score = num / denom
318			"""
319
320			def __init__(
321			self,
322			binary: bool = False,
323			background_weight: float = 0.0,
324			smooth_nr: float = EPS,
325			smooth_dr: float = EPS,
326			scales: Optional[List] = None,
327			kernel: str = "gaussian",
328			reduction: str = tf.keras.losses.Reduction.NONE,
329			name: str = "JaccardIndex",
330			):
331			"""
332			Init.
333
334			:param binary: if True, project y_true, y_pred to 0 or 1.
335			:param background_weight: weight for background, where y == 0.
336			:param smooth_nr: small constant added to numerator in case of zero covariance.
337			:param smooth_dr: small constant added to denominator in case of zero variance.
338			:param scales: list of scalars or None, if None, do not apply any scaling.
339			:param kernel: gaussian or cauchy.
340			:param reduction: using SUM reduction over batch axis,
341			this is for supporting multi-device training,
342			and the loss will be divided by global batch size,
343			calling the loss like `loss(y_true, y_pred)` will return a scalar tensor.
344			:param name: str, name of the loss.
345			"""
346			super().__init__(
347			binary=binary,
348			background_weight=background_weight,
349			smooth_nr=smooth_nr,
350			smooth_dr=smooth_dr,
351			scales=scales,
352			kernel=kernel,
353			reduction=reduction,
354			name=name,
355			)
356
357			def _call(self, y_true: tf.Tensor, y_pred: tf.Tensor) -> tf.Tensor:
358			"""
359			Return loss for a batch.
360
361			:param y_true: shape = (batch, ...)
362			:param y_pred: shape = (batch, ...)
363			:return: shape = (batch,)
364			"""
365			if self.binary:
366			y_true = tf.cast(y_true >= 0.5, dtype=y_true.dtype)
367			y_pred = tf.cast(y_pred >= 0.5, dtype=y_pred.dtype)
368
369			# (batch, ...) -> (batch, d)
370			y_true = self.flatten(y_true)
371			y_pred = self.flatten(y_pred)
372
373			# for foreground class
374			y_prod = tf.reduce_sum(y_true * y_pred, axis=1)
375			y_sum = tf.reduce_sum(y_true + y_pred, axis=1)
376
377			if self.background_weight > 0:
378			# generalized
379			vol = tf.reduce_sum(tf.ones_like(y_true), axis=1)
380			numerator = (
381			y_prod - self.background_weight * y_sum + self.background_weight * vol
382			)
383			denominator = (
384			(1 - self.background_weight) * y_sum
385			- y_prod
386			+ self.background_weight * vol
387			)
388			else:
389			# foreground only
390			numerator = y_prod
391			denominator = y_sum - y_prod
392
393			return (numerator + self.smooth_nr) / (denominator + self.smooth_dr)
394
395
396			@REGISTRY.register_loss(name="jaccard")
397			class JaccardLoss(NegativeLossMixin, JaccardIndex):
398			"""Revert the sign of JaccardIndex."""
399
400
401			def compute_centroid(mask: tf.Tensor, grid: tf.Tensor) -> tf.Tensor:
402			"""
403			Calculate the centroid of the mask.
404			:param mask: shape = (batch, dim1, dim2, dim3)
405			:param grid: shape = (1, dim1, dim2, dim3, 3)
406			:return: shape = (batch, 3), batch of vectors denoting
407			location of centroids.
408			"""
409			assert len(mask.shape) == 4
410			assert len(grid.shape) == 5
411			bool_mask = tf.expand_dims(
412			tf.cast(mask >= 0.5, dtype=tf.float32), axis=4
413			) # (batch, dim1, dim2, dim3, 1)
414			masked_grid = bool_mask * grid # (batch, dim1, dim2, dim3, 3)
415			numerator = tf.reduce_sum(masked_grid, axis=[1, 2, 3]) # (batch, 3)
416			denominator = tf.reduce_sum(bool_mask, axis=[1, 2, 3]) # (batch, 1)
417			return (numerator + EPS) / (denominator + EPS) # (batch, 3)
418
419
420			def compute_centroid_distance(
421			y_true: tf.Tensor, y_pred: tf.Tensor, grid: tf.Tensor
422			) -> tf.Tensor:
423			"""
424			Calculate the L2-distance between two tensors' centroids.
425			:param y_true: tensor, shape = (batch, dim1, dim2, dim3)
426			:param y_pred: tensor, shape = (batch, dim1, dim2, dim3)
427			:param grid: tensor, shape = (1, dim1, dim2, dim3, 3)
428			:return: shape = (batch,)
429			"""
430			centroid_1 = compute_centroid(mask=y_pred, grid=grid) # (batch, 3)
431			centroid_2 = compute_centroid(mask=y_true, grid=grid) # (batch, 3)
432			return tf.sqrt(tf.reduce_sum((centroid_1 - centroid_2) ** 2, axis=1))
433
434
435			def foreground_proportion(y: tf.Tensor) -> tf.Tensor:
436			"""
437			Calculate the percentage of foreground vs background per 3d volume.
438			:param y: shape = (batch, dim1, dim2, dim3), a 3D label tensor
439			:return: shape = (batch,)
440			"""
441			y = tf.cast(y >= 0.5, dtype=tf.float32)
442			return tf.reduce_sum(y, axis=[1, 2, 3]) / tf.reduce_sum(
443			tf.ones_like(y), axis=[1, 2, 3]
444			)
445

DeepRegNet / DeepReg

Pull Request — main (#736)

deepreg.loss.label.JaccardIndex.get_config() A

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