deepreg.dataset.preprocess.RandomDDFTransform3D.__init__() - Code Metrics - Inspection of "WIP 640 refactor model layers" - DeepRegNet/DeepReg - Measure and Improve Code Quality continuously with Scrutinizer

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Pull Request — main (#656)

by Yunguan

created 2021-02-20 13:24 UTC

RandomDDFTransform3D.init() A

↳ Parent: deepreg.dataset.preprocess

Complexity

Conditions

Size

Total Lines	41
Code Lines	19

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	19
dl	0
loc	41
rs	9.45
c	0
b	0
f	0
cc	1
nop	8

How to fix Many Parameters

"""
Module containing data augmentation techniques.
  - 3D Affine/DDF Transforms for moving and fixed images.
"""

from abc import abstractmethod
from typing import Dict

import numpy as np
import tensorflow as tf

from deepreg.model.layer import Resize3d
from deepreg.model.layer_util import get_reference_grid, resample, warp_grid
from deepreg.registry import REGISTRY


class RandomTransformation3D(tf.keras.layers.Layer):
    """
    An interface for different types of transformation.
    """

    def __init__(
        self,
        moving_image_size: tuple,
        fixed_image_size: tuple,
        batch_size: int,
        name: str = "RandomTransformation3D",
        trainable: bool = False,
    ):
        """
        Abstract class for image transformation.

        :param moving_image_size: (m_dim1, m_dim2, m_dim3)
        :param fixed_image_size: (f_dim1, f_dim2, f_dim3)
        :param batch_size: size of mini-batch
        :param name: name of layer
        :param trainable: if this layer is trainable
        """
        super().__init__(trainable=trainable, name=name)
        self.moving_image_size = moving_image_size
        self.fixed_image_size = fixed_image_size
        self.batch_size = batch_size
        self.moving_grid_ref = get_reference_grid(grid_size=moving_image_size)
        self.fixed_grid_ref = get_reference_grid(grid_size=fixed_image_size)

    @abstractmethod
    def gen_transform_params(self) -> (tf.Tensor, tf.Tensor):
        """
        Generates transformation parameters for moving and fixed image.

        :return: two tensors
        """

    @staticmethod
    @abstractmethod
    def transform(
        image: tf.Tensor, grid_ref: tf.Tensor, params: tf.Tensor
    ) -> tf.Tensor:
        """
        Transforms the reference grid and then resample the image.

        :param image: shape = (batch, dim1, dim2, dim3)
        :param grid_ref: shape = (dim1, dim2, dim3, 3)
        :param params: parameters for transformation
        :return: shape = (batch, dim1, dim2, dim3)
        """

    def call(self, inputs: Dict[str, tf.Tensor], **kwargs) -> Dict[str, tf.Tensor]:
        """
        Creates random params for the input images and their labels,
        and params them based on the resampled reference grids.
        :param inputs: a dict having multiple tensors
            if labeled:
                moving_image, shape = (batch, m_dim1, m_dim2, m_dim3)
                fixed_image, shape = (batch, f_dim1, f_dim2, f_dim3)
                moving_label, shape = (batch, m_dim1, m_dim2, m_dim3)
                fixed_label, shape = (batch, f_dim1, f_dim2, f_dim3)
                indices, shape = (batch, num_indices)
            else, unlabeled:
                moving_image, shape = (batch, m_dim1, m_dim2, m_dim3)
                fixed_image, shape = (batch, f_dim1, f_dim2, f_dim3)
                indices, shape = (batch, num_indices)
        :param kwargs: other arguments
        :return: dictionary with the same structure as inputs
        """

        moving_image = inputs["moving_image"]
        fixed_image = inputs["fixed_image"]
        indices = inputs["indices"]

        moving_params, fixed_params = self.gen_transform_params()

        moving_image = self.transform(moving_image, self.moving_grid_ref, moving_params)
        fixed_image = self.transform(fixed_image, self.fixed_grid_ref, fixed_params)

        if "moving_label" not in inputs:  # unlabeled
            return dict(
                moving_image=moving_image, fixed_image=fixed_image, indices=indices
            )
        moving_label = inputs["moving_label"]
        fixed_label = inputs["fixed_label"]

        moving_label = self.transform(moving_label, self.moving_grid_ref, moving_params)
        fixed_label = self.transform(fixed_label, self.fixed_grid_ref, fixed_params)

        return dict(
            moving_image=moving_image,
            fixed_image=fixed_image,
            moving_label=moving_label,
            fixed_label=fixed_label,
            indices=indices,
        )

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


@REGISTRY.register_data_augmentation(name="affine")
class RandomAffineTransform3D(RandomTransformation3D):
    """Apply random affine transformation to moving/fixed images separately."""

    def __init__(
        self,
        moving_image_size: tuple,
        fixed_image_size: tuple,
        batch_size: int,
        scale: float = 0.1,
        name: str = "RandomAffineTransform3D",
        **kwargs,
    ):
        """
        Init.

        :param moving_image_size: (m_dim1, m_dim2, m_dim3)
        :param fixed_image_size: (f_dim1, f_dim2, f_dim3)
        :param batch_size: size of mini-batch
        :param scale: a positive float controlling the scale of transformation
        :param name: name of the layer
        :param kwargs: extra arguments
        """
        super().__init__(
            moving_image_size=moving_image_size,
            fixed_image_size=fixed_image_size,
            batch_size=batch_size,
            name=name,
            **kwargs,
        )
        self.scale = scale

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

    def gen_transform_params(self) -> (tf.Tensor, tf.Tensor):
        """
        Function that generates the random 3D transformation parameters
        for a batch of data for moving and fixed image.

        :return: a tuple of tensors, each has shape = (batch, 4, 3)
        """
        theta = gen_rand_affine_transform(
            batch_size=self.batch_size * 2, scale=self.scale
        )
        return theta[: self.batch_size], theta[self.batch_size :]

    @staticmethod
    def transform(
        image: tf.Tensor, grid_ref: tf.Tensor, params: tf.Tensor
    ) -> tf.Tensor:
        """
        Transforms the reference grid and then resample the image.

        :param image: shape = (batch, dim1, dim2, dim3)
        :param grid_ref: shape = (dim1, dim2, dim3, 3)
        :param params: shape = (batch, 4, 3)
        :return: shape = (batch, dim1, dim2, dim3)
        """
        return resample(vol=image, loc=warp_grid(grid_ref, params))


@REGISTRY.register_data_augmentation(name="ddf")
class RandomDDFTransform3D(RandomTransformation3D):
    """Apply random DDF transformation to moving/fixed images separately."""

    def __init__(
        self,
        moving_image_size: tuple,
        fixed_image_size: tuple,
        batch_size: int,
        field_strength: int = 1,
        low_res_size: tuple = (1, 1, 1),
        name: str = "RandomDDFTransform3D",
        **kwargs,
    ):
        """
        Creates a DDF transformation for data augmentation.

        To simulate smooth deformation fields, we interpolate from a low resolution
        field of size low_res_size using linear interpolation. The variance of the
        deformation field is drawn from a uniform variable
        between [0, field_strength].

        :param moving_image_size: tuple
        :param fixed_image_size: tuple
        :param batch_size: int
        :param field_strength: int = 1. It is used as the upper bound for the
        deformation field variance
        :param low_res_size: tuple = (1, 1, 1).
        :param name: name of layer
        :param kwargs: extra arguments
        """

        super().__init__(
            moving_image_size=moving_image_size,
            fixed_image_size=fixed_image_size,
            batch_size=batch_size,
            name=name,
            **kwargs,
        )

        assert tuple(low_res_size) <= tuple(moving_image_size)
        assert tuple(low_res_size) <= tuple(fixed_image_size)

        self.field_strength = field_strength
        self.low_res_size = low_res_size

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

    def gen_transform_params(self) -> (tf.Tensor, tf.Tensor):
        """
        Generates two random ddf fields for moving and fixed images.

        :return: tuple, one has shape = (batch, m_dim1, m_dim2, m_dim3, 3)
            another one has shape = (batch, f_dim1, f_dim2, f_dim3, 3)
        """
        kwargs = dict(
            batch_size=self.batch_size,
            field_strength=self.field_strength,
            low_res_size=self.low_res_size,
        )
        moving = gen_rand_ddf(image_size=self.moving_image_size, **kwargs)
        fixed = gen_rand_ddf(image_size=self.fixed_image_size, **kwargs)
        return moving, fixed

    @staticmethod
    def transform(
        image: tf.Tensor, grid_ref: tf.Tensor, params: tf.Tensor
    ) -> tf.Tensor:
        """
        Transforms the reference grid and then resample the image.

        :param image: shape = (batch, dim1, dim2, dim3)
        :param grid_ref: shape = (dim1, dim2, dim3, 3)
        :param params: DDF, shape = (batch, dim1, dim2, dim3, 3)
        :return: shape = (batch, dim1, dim2, dim3)
        """
        return resample(vol=image, loc=grid_ref[None, ...] + params)


def resize_inputs(
    inputs: Dict[str, tf.Tensor], moving_image_size: tuple, fixed_image_size: tuple
) -> Dict[str, tf.Tensor]:
    """
    Resize inputs
    :param inputs:
        if labeled:
            moving_image, shape = (None, None, None)
            fixed_image, shape = (None, None, None)
            moving_label, shape = (None, None, None)
            fixed_label, shape = (None, None, None)
            indices, shape = (num_indices, )
        else, unlabeled:
            moving_image, shape = (None, None, None)
            fixed_image, shape = (None, None, None)
            indices, shape = (num_indices, )
    :param moving_image_size: tuple, (m_dim1, m_dim2, m_dim3)
    :param fixed_image_size: tuple, (f_dim1, f_dim2, f_dim3)
    :return:
        if labeled:
            moving_image, shape = (m_dim1, m_dim2, m_dim3)
            fixed_image, shape = (f_dim1, f_dim2, f_dim3)
            moving_label, shape = (m_dim1, m_dim2, m_dim3)
            fixed_label, shape = (f_dim1, f_dim2, f_dim3)
            indices, shape = (num_indices, )
        else, unlabeled:
            moving_image, shape = (m_dim1, m_dim2, m_dim3)
            fixed_image, shape = (f_dim1, f_dim2, f_dim3)
            indices, shape = (num_indices, )
    """
    moving_image = inputs["moving_image"]
    fixed_image = inputs["fixed_image"]
    indices = inputs["indices"]

    moving_resize_layer = Resize3d(shape=moving_image_size)
    fixed_resize_layer = Resize3d(shape=fixed_image_size)

    moving_image = moving_resize_layer(moving_image)
    fixed_image = fixed_resize_layer(fixed_image)

    if "moving_label" not in inputs:  # unlabeled
        return dict(moving_image=moving_image, fixed_image=fixed_image, indices=indices)
    moving_label = inputs["moving_label"]
    fixed_label = inputs["fixed_label"]

    moving_label = moving_resize_layer(moving_label)
    fixed_label = fixed_resize_layer(fixed_label)

    return dict(
        moving_image=moving_image,
        fixed_image=fixed_image,
        moving_label=moving_label,
        fixed_label=fixed_label,
        indices=indices,
    )


def gen_rand_affine_transform(
    batch_size: int, scale: float, seed: (int, None) = None
) -> tf.Tensor:
    """
    Function that generates a random 3D transformation parameters for a batch of data.

    for 3D coordinates, affine transformation is

    .. code-block:: text

        [[x' y' z' 1]] = [[x y z 1]] * [[* * * 0]
                                        [* * * 0]
                                        [* * * 0]
                                        [* * * 1]]

    where each * represents a degree of freedom,
    so there are in total 12 degrees of freedom
    the equation can be denoted as

        new = old * T

    where

    - new is the transformed coordinates, of shape (1, 4)
    - old is the original coordinates, of shape (1, 4)
    - T is the transformation matrix, of shape (4, 4)

    the equation can be simplified to

    .. code-block:: text

        [[x' y' z']] = [[x y z 1]] * [[* * *]
                                      [* * *]
                                      [* * *]
                                      [* * *]]

    so that

        new = old * T

    where

    - new is the transformed coordinates, of shape (1, 3)
    - old is the original coordinates, of shape (1, 4)
    - T is the transformation matrix, of shape (4, 3)

    Given original and transformed coordinates,
    we can calculate the transformation matrix using

        x = np.linalg.lstsq(a, b)

    such that

        a x = b

    In our case,

    - a = old
    - b = new
    - x = T

    To generate random transformation,
    we choose to add random perturbation to corner coordinates as follows:
    for corner of coordinates (x, y, z), the noise is

        -(x, y, z) .* (r1, r2, r3)

    where ri is a random number between (0, scale).
    So

        (x', y', z') = (x, y, z) .* (1-r1, 1-r2, 1-r3)

    Thus, we can directly sample between 1-scale and 1 instead

    We choose to calculate the transformation based on
    four corners in a cube centered at (0, 0, 0).
    A cube is shown as below, where

    - C = (-1, -1, -1)
    - G = (-1, -1, 1)
    - D = (-1, 1, -1)
    - A = (1, -1, -1)

    .. code-block:: text

                    G — — — — — — — — H
                  / |               / |
                /   |             /   |
              /     |           /     |
            /       |         /       |
          /         |       /         |
        E — — — — — — — — F           |
        |           |     |           |
        |           |     |           |
        |           C — — | — — — — — D
        |         /       |         /
        |       /         |       /
        |     /           |     /
        |   /             |   /
        | /               | /
        A — — — — — — — — B

    :param batch_size: int
    :param scale: a float number between 0 and 1
    :param seed: control the randomness
    :return: shape = (batch, 4, 3)
    """

    assert 0 <= scale <= 1
    np.random.seed(seed)
    noise = np.random.uniform(1 - scale, 1, [batch_size, 4, 3])  # shape = (batch, 4, 3)

    # old represents four corners of a cube
    # corresponding to the corner C G D A as shown above
    old = np.tile(
        [[[-1, -1, -1, 1], [-1, -1, 1, 1], [-1, 1, -1, 1], [1, -1, -1, 1]]],
        [batch_size, 1, 1],
    )  # shape = (batch, 4, 4)
    new = old[:, :, :3] * noise  # shape = (batch, 4, 3)

    theta = np.array(
        [np.linalg.lstsq(old[k], new[k], rcond=-1)[0] for k in range(batch_size)]
    )  # shape = (batch, 4, 3)

    return tf.cast(theta, dtype=tf.float32)


def gen_rand_ddf(
    batch_size: int,
    image_size: tuple,
    field_strength: (tuple, list),
    low_res_size: (tuple, list),
    seed: (int, None) = None,
) -> tf.Tensor:
    """
    Function that generates a random 3D DDF for a batch of data.

    :param batch_size:
    :param image_size:
    :param field_strength: maximum field strength, computed as a U[0,field_strength]
    :param low_res_size: low_resolution deformation field that will be upsampled to
        the original size in order to get smooth and more realistic fields.
    :param seed: control the randomness
    :return:
    """

    np.random.seed(seed)
    low_res_strength = np.random.uniform(0, field_strength, (batch_size, 1, 1, 1, 3))
    low_res_field = low_res_strength * np.random.randn(
        batch_size, low_res_size[0], low_res_size[1], low_res_size[2], 3
    )
    high_res_field = Resize3d(shape=image_size)(low_res_field)
    return high_res_field


1			"""
2			Module containing data augmentation techniques.
3			- 3D Affine/DDF Transforms for moving and fixed images.
4			"""
5
6			from abc import abstractmethod
7			from typing import Dict
8
9			import numpy as np
10			import tensorflow as tf
11
12			from deepreg.model.layer import Resize3d
13			from deepreg.model.layer_util import get_reference_grid, resample, warp_grid
14			from deepreg.registry import REGISTRY
15
16
17			class RandomTransformation3D(tf.keras.layers.Layer):
18			"""
19			An interface for different types of transformation.
20			"""
21
22			def __init__(
23			self,
24			moving_image_size: tuple,
25			fixed_image_size: tuple,
26			batch_size: int,
27			name: str = "RandomTransformation3D",
28			trainable: bool = False,
29			):
30			"""
31			Abstract class for image transformation.
32
33			:param moving_image_size: (m_dim1, m_dim2, m_dim3)
34			:param fixed_image_size: (f_dim1, f_dim2, f_dim3)
35			:param batch_size: size of mini-batch
36			:param name: name of layer
37			:param trainable: if this layer is trainable
38			"""
39			super().__init__(trainable=trainable, name=name)
40			self.moving_image_size = moving_image_size
41			self.fixed_image_size = fixed_image_size
42			self.batch_size = batch_size
43			self.moving_grid_ref = get_reference_grid(grid_size=moving_image_size)
44			self.fixed_grid_ref = get_reference_grid(grid_size=fixed_image_size)
45
46			@abstractmethod
47			def gen_transform_params(self) -> (tf.Tensor, tf.Tensor):
48			"""
49			Generates transformation parameters for moving and fixed image.
50
51			:return: two tensors
52			"""
53
54			@staticmethod
55			@abstractmethod
56			def transform(
57			image: tf.Tensor, grid_ref: tf.Tensor, params: tf.Tensor
58			) -> tf.Tensor:
59			"""
60			Transforms the reference grid and then resample the image.
61
62			:param image: shape = (batch, dim1, dim2, dim3)
63			:param grid_ref: shape = (dim1, dim2, dim3, 3)
64			:param params: parameters for transformation
65			:return: shape = (batch, dim1, dim2, dim3)
66			"""
67
68			def call(self, inputs: Dict[str, tf.Tensor], **kwargs) -> Dict[str, tf.Tensor]:
69			"""
70			Creates random params for the input images and their labels,
71			and params them based on the resampled reference grids.
72			:param inputs: a dict having multiple tensors
73			if labeled:
74			moving_image, shape = (batch, m_dim1, m_dim2, m_dim3)
75			fixed_image, shape = (batch, f_dim1, f_dim2, f_dim3)
76			moving_label, shape = (batch, m_dim1, m_dim2, m_dim3)
77			fixed_label, shape = (batch, f_dim1, f_dim2, f_dim3)
78			indices, shape = (batch, num_indices)
79			else, unlabeled:
80			moving_image, shape = (batch, m_dim1, m_dim2, m_dim3)
81			fixed_image, shape = (batch, f_dim1, f_dim2, f_dim3)
82			indices, shape = (batch, num_indices)
83			:param kwargs: other arguments
84			:return: dictionary with the same structure as inputs
85			"""
86
87			moving_image = inputs["moving_image"]
88			fixed_image = inputs["fixed_image"]
89			indices = inputs["indices"]
90
91			moving_params, fixed_params = self.gen_transform_params()
92
93			moving_image = self.transform(moving_image, self.moving_grid_ref, moving_params)
94			fixed_image = self.transform(fixed_image, self.fixed_grid_ref, fixed_params)
95
96			if "moving_label" not in inputs: # unlabeled
97			return dict(
98			moving_image=moving_image, fixed_image=fixed_image, indices=indices
99			)
100			moving_label = inputs["moving_label"]
101			fixed_label = inputs["fixed_label"]
102
103			moving_label = self.transform(moving_label, self.moving_grid_ref, moving_params)
104			fixed_label = self.transform(fixed_label, self.fixed_grid_ref, fixed_params)
105
106			return dict(
107			moving_image=moving_image,
108			fixed_image=fixed_image,
109			moving_label=moving_label,
110			fixed_label=fixed_label,
111			indices=indices,
112			)
113
114			def get_config(self) -> dict:
115			"""Return the config dictionary for recreating this class."""
116			config = super().get_config()
117			config["moving_image_size"] = self.moving_image_size
118			config["fixed_image_size"] = self.fixed_image_size
119			config["batch_size"] = self.batch_size
120			return config
121
122
123			@REGISTRY.register_data_augmentation(name="affine")
124			class RandomAffineTransform3D(RandomTransformation3D):
125			"""Apply random affine transformation to moving/fixed images separately."""
126
127			def __init__(
128			self,
129			moving_image_size: tuple,
130			fixed_image_size: tuple,
131			batch_size: int,
132			scale: float = 0.1,
133			name: str = "RandomAffineTransform3D",
134			**kwargs,
135			):
136			"""
137			Init.
138
139			:param moving_image_size: (m_dim1, m_dim2, m_dim3)
140			:param fixed_image_size: (f_dim1, f_dim2, f_dim3)
141			:param batch_size: size of mini-batch
142			:param scale: a positive float controlling the scale of transformation
143			:param name: name of the layer
144			:param kwargs: extra arguments
145			"""
146			super().__init__(
147			moving_image_size=moving_image_size,
148			fixed_image_size=fixed_image_size,
149			batch_size=batch_size,
150			name=name,
151			**kwargs,
152			)
153			self.scale = scale
154
155			def get_config(self) -> dict:
156			"""Return the config dictionary for recreating this class."""
157			config = super().get_config()
158			config["scale"] = self.scale
159			return config
160
161			def gen_transform_params(self) -> (tf.Tensor, tf.Tensor):
162			"""
163			Function that generates the random 3D transformation parameters
164			for a batch of data for moving and fixed image.
165
166			:return: a tuple of tensors, each has shape = (batch, 4, 3)
167			"""
168			theta = gen_rand_affine_transform(
169			batch_size=self.batch_size * 2, scale=self.scale
170			)
171			return theta[: self.batch_size], theta[self.batch_size :]
172
173			@staticmethod
174			def transform(
175			image: tf.Tensor, grid_ref: tf.Tensor, params: tf.Tensor
176			) -> tf.Tensor:
177			"""
178			Transforms the reference grid and then resample the image.
179
180			:param image: shape = (batch, dim1, dim2, dim3)
181			:param grid_ref: shape = (dim1, dim2, dim3, 3)
182			:param params: shape = (batch, 4, 3)
183			:return: shape = (batch, dim1, dim2, dim3)
184			"""
185			return resample(vol=image, loc=warp_grid(grid_ref, params))
186
187
188			@REGISTRY.register_data_augmentation(name="ddf")
189			class RandomDDFTransform3D(RandomTransformation3D):
190			"""Apply random DDF transformation to moving/fixed images separately."""
191
192			def __init__(
193			self,
194			moving_image_size: tuple,
195			fixed_image_size: tuple,
196			batch_size: int,
197			field_strength: int = 1,
198			low_res_size: tuple = (1, 1, 1),
199			name: str = "RandomDDFTransform3D",
200			**kwargs,
201			):
202			"""
203			Creates a DDF transformation for data augmentation.
204
205			To simulate smooth deformation fields, we interpolate from a low resolution
206			field of size low_res_size using linear interpolation. The variance of the
207			deformation field is drawn from a uniform variable
208			between [0, field_strength].
209
210			:param moving_image_size: tuple
211			:param fixed_image_size: tuple
212			:param batch_size: int
213			:param field_strength: int = 1. It is used as the upper bound for the
214			deformation field variance
215			:param low_res_size: tuple = (1, 1, 1).
216			:param name: name of layer
217			:param kwargs: extra arguments
218			"""
219
220			super().__init__(
221			moving_image_size=moving_image_size,
222			fixed_image_size=fixed_image_size,
223			batch_size=batch_size,
224			name=name,
225			**kwargs,
226			)
227
228			assert tuple(low_res_size) <= tuple(moving_image_size)
229			assert tuple(low_res_size) <= tuple(fixed_image_size)
230
231			self.field_strength = field_strength
232			self.low_res_size = low_res_size
233
234			def get_config(self) -> dict:
235			"""Return the config dictionary for recreating this class."""
236			config = super().get_config()
237			config["field_strength"] = self.field_strength
238			config["low_res_size"] = self.low_res_size
239			return config
240
241			def gen_transform_params(self) -> (tf.Tensor, tf.Tensor):
242			"""
243			Generates two random ddf fields for moving and fixed images.
244
245			:return: tuple, one has shape = (batch, m_dim1, m_dim2, m_dim3, 3)
246			another one has shape = (batch, f_dim1, f_dim2, f_dim3, 3)
247			"""
248			kwargs = dict(
249			batch_size=self.batch_size,
250			field_strength=self.field_strength,
251			low_res_size=self.low_res_size,
252			)
253			moving = gen_rand_ddf(image_size=self.moving_image_size, **kwargs)
254			fixed = gen_rand_ddf(image_size=self.fixed_image_size, **kwargs)
255			return moving, fixed
256
257			@staticmethod
258			def transform(
259			image: tf.Tensor, grid_ref: tf.Tensor, params: tf.Tensor
260			) -> tf.Tensor:
261			"""
262			Transforms the reference grid and then resample the image.
263
264			:param image: shape = (batch, dim1, dim2, dim3)
265			:param grid_ref: shape = (dim1, dim2, dim3, 3)
266			:param params: DDF, shape = (batch, dim1, dim2, dim3, 3)
267			:return: shape = (batch, dim1, dim2, dim3)
268			"""
269			return resample(vol=image, loc=grid_ref[None, ...] + params)
270
271
272			def resize_inputs(
273			inputs: Dict[str, tf.Tensor], moving_image_size: tuple, fixed_image_size: tuple
274			) -> Dict[str, tf.Tensor]:
275			"""
276			Resize inputs
277			:param inputs:
278			if labeled:
279			moving_image, shape = (None, None, None)
280			fixed_image, shape = (None, None, None)
281			moving_label, shape = (None, None, None)
282			fixed_label, shape = (None, None, None)
283			indices, shape = (num_indices, )
284			else, unlabeled:
285			moving_image, shape = (None, None, None)
286			fixed_image, shape = (None, None, None)
287			indices, shape = (num_indices, )
288			:param moving_image_size: tuple, (m_dim1, m_dim2, m_dim3)
289			:param fixed_image_size: tuple, (f_dim1, f_dim2, f_dim3)
290			:return:
291			if labeled:
292			moving_image, shape = (m_dim1, m_dim2, m_dim3)
293			fixed_image, shape = (f_dim1, f_dim2, f_dim3)
294			moving_label, shape = (m_dim1, m_dim2, m_dim3)
295			fixed_label, shape = (f_dim1, f_dim2, f_dim3)
296			indices, shape = (num_indices, )
297			else, unlabeled:
298			moving_image, shape = (m_dim1, m_dim2, m_dim3)
299			fixed_image, shape = (f_dim1, f_dim2, f_dim3)
300			indices, shape = (num_indices, )
301			"""
302			moving_image = inputs["moving_image"]
303			fixed_image = inputs["fixed_image"]
304			indices = inputs["indices"]
305
306			moving_resize_layer = Resize3d(shape=moving_image_size)
307			fixed_resize_layer = Resize3d(shape=fixed_image_size)
308
309			moving_image = moving_resize_layer(moving_image)
310			fixed_image = fixed_resize_layer(fixed_image)
311
312			if "moving_label" not in inputs: # unlabeled
313			return dict(moving_image=moving_image, fixed_image=fixed_image, indices=indices)
314			moving_label = inputs["moving_label"]
315			fixed_label = inputs["fixed_label"]
316
317			moving_label = moving_resize_layer(moving_label)
318			fixed_label = fixed_resize_layer(fixed_label)
319
320			return dict(
321			moving_image=moving_image,
322			fixed_image=fixed_image,
323			moving_label=moving_label,
324			fixed_label=fixed_label,
325			indices=indices,
326			)
327
328
329			def gen_rand_affine_transform(
330			batch_size: int, scale: float, seed: (int, None) = None
331			) -> tf.Tensor:
332			"""
333			Function that generates a random 3D transformation parameters for a batch of data.
334
335			for 3D coordinates, affine transformation is
336
337			.. code-block:: text
338
339			[[x' y' z' 1]] = [[x y z 1]] * [[* * * 0]
340			[* * * 0]
341			[* * * 0]
342			[* * * 1]]
343
344			where each * represents a degree of freedom,
345			so there are in total 12 degrees of freedom
346			the equation can be denoted as
347
348			new = old * T
349
350			where
351
352			- new is the transformed coordinates, of shape (1, 4)
353			- old is the original coordinates, of shape (1, 4)
354			- T is the transformation matrix, of shape (4, 4)
355
356			the equation can be simplified to
357
358			.. code-block:: text
359
360			[[x' y' z']] = [[x y z 1]] * [[* * *]
361			[* * *]
362			[* * *]
363			[* * *]]
364
365			so that
366
367			new = old * T
368
369			where
370
371			- new is the transformed coordinates, of shape (1, 3)
372			- old is the original coordinates, of shape (1, 4)
373			- T is the transformation matrix, of shape (4, 3)
374
375			Given original and transformed coordinates,
376			we can calculate the transformation matrix using
377
378			x = np.linalg.lstsq(a, b)
379
380			such that
381
382			a x = b
383
384			In our case,
385
386			- a = old
387			- b = new
388			- x = T
389
390			To generate random transformation,
391			we choose to add random perturbation to corner coordinates as follows:
392			for corner of coordinates (x, y, z), the noise is
393
394			-(x, y, z) .* (r1, r2, r3)
395
396			where ri is a random number between (0, scale).
397			So
398
399			(x', y', z') = (x, y, z) .* (1-r1, 1-r2, 1-r3)
400
401			Thus, we can directly sample between 1-scale and 1 instead
402
403			We choose to calculate the transformation based on
404			four corners in a cube centered at (0, 0, 0).
405			A cube is shown as below, where
406
407			- C = (-1, -1, -1)
408			- G = (-1, -1, 1)
409			- D = (-1, 1, -1)
410			- A = (1, -1, -1)
411
412			.. code-block:: text
413
414			G — — — — — — — — H
415			/ \| / \|
416			/ \| / \|
417			/ \| / \|
418			/ \| / \|
419			/ \| / \|
420			E — — — — — — — — F \|
421			\| \| \| \|
422			\| \| \| \|
423			\| C — — \| — — — — — D
424			\| / \| /
425			\| / \| /
426			\| / \| /
427			\| / \| /
428			\| / \| /
429			A — — — — — — — — B
430
431			:param batch_size: int
432			:param scale: a float number between 0 and 1
433			:param seed: control the randomness
434			:return: shape = (batch, 4, 3)
435			"""
436
437			assert 0 <= scale <= 1
438			np.random.seed(seed)
439			noise = np.random.uniform(1 - scale, 1, [batch_size, 4, 3]) # shape = (batch, 4, 3)
440
441			# old represents four corners of a cube
442			# corresponding to the corner C G D A as shown above
443			old = np.tile(
444			[[[-1, -1, -1, 1], [-1, -1, 1, 1], [-1, 1, -1, 1], [1, -1, -1, 1]]],
445			[batch_size, 1, 1],
446			) # shape = (batch, 4, 4)
447			new = old[:, :, :3] * noise # shape = (batch, 4, 3)
448
449			theta = np.array(
450			[np.linalg.lstsq(old[k], new[k], rcond=-1)[0] for k in range(batch_size)]
451			) # shape = (batch, 4, 3)
452
453			return tf.cast(theta, dtype=tf.float32)
454
455
456			def gen_rand_ddf(
457			batch_size: int,
458			image_size: tuple,
459			field_strength: (tuple, list),
460			low_res_size: (tuple, list),
461			seed: (int, None) = None,
462			) -> tf.Tensor:
463			"""
464			Function that generates a random 3D DDF for a batch of data.
465
466			:param batch_size:
467			:param image_size:
468			:param field_strength: maximum field strength, computed as a U[0,field_strength]
469			:param low_res_size: low_resolution deformation field that will be upsampled to
470			the original size in order to get smooth and more realistic fields.
471			:param seed: control the randomness
472			:return:
473			"""
474
475			np.random.seed(seed)
476			low_res_strength = np.random.uniform(0, field_strength, (batch_size, 1, 1, 1, 3))
477			low_res_field = low_res_strength * np.random.randn(
478			batch_size, low_res_size[0], low_res_size[1], low_res_size[2], 3
479			)
480			high_res_field = Resize3d(shape=image_size)(low_res_field)
481			return high_res_field
482

DeepRegNet / DeepReg

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