deepreg.model.layer.Deconv3d.__init__() - Code Metrics - Inspection of "WIP 640 refactor model layers" - DeepRegNet/DeepReg - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Pull Request — main (#656)

by Yunguan

created 2021-02-02 22:03 UTC

deepreg.model.layer.Deconv3d.init() A

↳ Parent: deepreg.model.layer

Complexity

Conditions

Size

Total Lines	34
Code Lines	19

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	19
dl	0
loc	34
rs	9.45
c	0
b	0
f	0
cc	1
nop	8

How to fix Many Parameters

"""This module defines custom layers."""
import itertools

import numpy as np
import tensorflow as tf
import tensorflow.keras.layers as tfkl

import deepreg.model.layer_util as layer_util

LAYER_DICT = dict(conv3d=tfkl.Conv3D, deconv3d=tfkl.Conv3DTranspose)
NORM_DICT = dict(batch=tfkl.BatchNormalization, layer=tfkl.LayerNormalization)


class NormBlock(tfkl.Layer):
    """
    A block with layer - norm - activation.
    """

    def __init__(
        self,
        layer_name: str,
        norm_name: str = "batch",
        activation: str = "relu",
        name: str = "norm_block",
        **kwargs,
    ):
        """
        Init.

        :param layer_name: class of the layer to be wrapped.
        :param norm_name: class of the normalization layer.
        :param activation: name of activation.
        :param name: name of the block layer.
        :param kwargs: additional arguments.
        """
        super().__init__()
        self._config = dict(
            layer_name=layer_name,
            norm_name=norm_name,
            activation=activation,
            name=name,
            **kwargs,
        )
        self._layer = LAYER_DICT[layer_name](use_bias=False, **kwargs)
        self._norm = NORM_DICT[norm_name]()
        self._act = tfkl.Activation(activation=activation)

    def call(self, inputs, training=None, **kwargs) -> tf.Tensor:

        """
        Forward.

        :param inputs: inputs for the layer
        :param training: training flag for normalization layers (default: None)
        :param kwargs: additional arguments.
        :return:
        """
        output = self._layer(inputs=inputs)
        output = self._norm(inputs=output, training=training)
        output = self._act(output)
        return output

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


class Conv3dBlock(NormBlock):
    """
    A conv3d block having conv3d - norm - activation.
    """

    def __init__(
        self,
        name: str = "conv3d_block",
        **kwargs,
    ):
        """
        Init.

        :param name: name of the layer
        :param kwargs: additional arguments.
        """
        super().__init__(layer_name="conv3d", name=name, **kwargs)


class Deconv3dBlock(NormBlock):
    """
    A deconv3d block having conv3d - norm - activation.
    """

    def __init__(
        self,
        name: str = "deconv3d_block",
        **kwargs,
    ):
        """
        Init.

        :param name: name of the layer
        :param kwargs: additional arguments.
        """
        super().__init__(layer_name="deconv3d", name=name, **kwargs)


class Resize3d(tfkl.Layer):
    """
    Resize image in two folds.

    - resize dim2 and dim3
    - resize dim1 and dim2
    """

    def __init__(
        self,
        shape: tuple,
        method: str = tf.image.ResizeMethod.BILINEAR,
        name: str = "resize3d",
    ):
        """
        Init, save arguments.

        :param shape: (dim1, dim2, dim3)
        :param method: tf.image.ResizeMethod
        :param name: name of the layer
        """
        super().__init__(name=name)
        assert len(shape) == 3
        self._shape = shape
        self._method = method

    def call(self, inputs: tf.Tensor, **kwargs) -> tf.Tensor:

        """
        Perform two fold resize.

        :param inputs: shape = (batch, dim1, dim2, dim3, channels)
                                     or (batch, dim1, dim2, dim3)
                                     or (dim1, dim2, dim3)
        :param kwargs: additional arguments
        :return: shape = (batch, out_dim1, out_dim2, out_dim3, channels)
                                or (batch, dim1, dim2, dim3)
                                or (dim1, dim2, dim3)
        """
        # sanity check
        image = inputs
        image_dim = len(image.shape)

        # init
        if image_dim == 5:
            has_channel = True
            has_batch = True
            input_image_shape = image.shape[1:4]
        elif image_dim == 4:
            has_channel = False
            has_batch = True
            input_image_shape = image.shape[1:4]
        elif image_dim == 3:
            has_channel = False
            has_batch = False
            input_image_shape = image.shape[0:3]
        else:
            raise ValueError(
                "Resize3d takes input image of dimension 3 or 4 or 5, "
                "corresponding to (dim1, dim2, dim3) "
                "or (batch, dim1, dim2, dim3) "
                "or (batch, dim1, dim2, dim3, channels), "
                "got image shape{}".format(image.shape)
            )

        # no need of resize
        if input_image_shape == tuple(self._shape):
            return image

        # expand to five dimensions
        if not has_batch:
            image = tf.expand_dims(image, axis=0)
        if not has_channel:
            image = tf.expand_dims(image, axis=-1)
        assert len(image.shape) == 5  # (batch, dim1, dim2, dim3, channels)
        image_shape = tf.shape(image)

        # merge axis 0 and 1
        output = tf.reshape(
            image, (-1, image_shape[2], image_shape[3], image_shape[4])
        )  # (batch * dim1, dim2, dim3, channels)

        # resize dim2 and dim3
        output = tf.image.resize(
            images=output, size=self._shape[1:3], method=self._method
        )  # (batch * dim1, out_dim2, out_dim3, channels)

        # split axis 0 and merge axis 3 and 4
        output = tf.reshape(
            output,
            shape=(-1, image_shape[1], self._shape[1], self._shape[2] * image_shape[4]),
        )  # (batch, dim1, out_dim2, out_dim3 * channels)

        # resize dim1 and dim2
        output = tf.image.resize(
            images=output, size=self._shape[:2], method=self._method
        )  # (batch, out_dim1, out_dim2, out_dim3 * channels)

        # reshape
        output = tf.reshape(
            output, shape=[-1, *self._shape, image_shape[4]]
        )  # (batch, out_dim1, out_dim2, out_dim3, channels)

        # squeeze to original dimension
        if not has_batch:
            output = tf.squeeze(output, axis=0)
        if not has_channel:
            output = tf.squeeze(output, axis=-1)
        return output

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


class Warping(tfkl.Layer):
    """
    Warps an image with DDF.

    Reference:

    https://github.com/adalca/neurite/blob/legacy/neuron/utils.py
    where vol = image, loc_shift = ddf
    """

    def __init__(self, fixed_image_size: tuple, name: str = "warping", **kwargs):
        """
        Init.

        :param fixed_image_size: shape = (f_dim1, f_dim2, f_dim3)
             or (f_dim1, f_dim2, f_dim3, ch) with the last channel for features
        :param name: name of the layer
        :param kwargs: additional arguments.
        """
        super().__init__(name=name, **kwargs)
        self._fixed_image_size = fixed_image_size
        # shape = (1, f_dim1, f_dim2, f_dim3, 3)
        self.grid_ref = layer_util.get_reference_grid(grid_size=fixed_image_size)
        self.grid_ref = self.grid_ref[None, ...]

    def call(self, inputs, **kwargs) -> tf.Tensor:

        """
        :param inputs: (ddf, image)

          - ddf, shape = (batch, f_dim1, f_dim2, f_dim3, 3)
          - image, shape = (batch, m_dim1, m_dim2, m_dim3)
        :param kwargs: additional arguments.
        :return: shape = (batch, f_dim1, f_dim2, f_dim3)
        """
        ddf, image = inputs
        return layer_util.resample(vol=image, loc=self.grid_ref + ddf)

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


class ResidualBlock(tfkl.Layer):
    """
    A block with skip links and layer - norm - activation.
    """

    def __init__(
        self,
        layer_name: str,
        num_layers: int = 2,
        norm_name: str = "batch",
        activation: str = "relu",
        name: str = "res_block",
        **kwargs,
    ):
        """
        Init.

        :param layer_name: class of the layer to be wrapped.
        :param num_layers: number of layers/blocks.
        :param norm_name: class of the normalization layer.
        :param activation: name of activation.
        :param name: name of the block layer.
        :param kwargs: additional arguments.
        """
        super().__init__()
        self._num_layers = num_layers
        self._config = dict(
            layer_name=layer_name,
            num_layers=num_layers,
            norm_name=norm_name,
            activation=activation,
            name=name,
            **kwargs,
        )
        self._layers = [
            LAYER_DICT[layer_name](use_bias=False, **kwargs) for _ in range(num_layers)
        ]
        self._norms = [NORM_DICT[norm_name]() for _ in range(num_layers)]
        self._acts = [tfkl.Activation(activation=activation) for _ in range(num_layers)]

    def call(self, inputs, training=None, **kwargs) -> tf.Tensor:

        """
        Forward.

        :param inputs: inputs for the layer
        :param training: training flag for normalization layers (default: None)
        :param kwargs: additional arguments.
        :return:
        """

        output = inputs
        for i in range(self._num_layers):
            output = self._layers[i](inputs=output)
            output = self._norms[i](inputs=output, training=training)
            if i == self._num_layers - 1:
                # last block
                output = output + inputs
            output = self._acts[i](output)
        return output

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


class ResidualConv3dBlock(ResidualBlock):
    """
    A conv3d residual block
    """

    def __init__(
        self,
        name: str = "conv3d_res_block",
        **kwargs,
    ):
        """
        Init.

        :param name: name of the layer
        :param kwargs: additional arguments.
        """
        super().__init__(layer_name="conv3d", name=name, **kwargs)


class IntDVF(tfkl.Layer):
    """
    Integrate DVF to get DDF.

    Reference:

    - integrate_vec of neuron
      https://github.com/adalca/neurite/blob/legacy/neuron/utils.py
    """

    def __init__(
        self,
        fixed_image_size: tuple,
        num_steps: int = 7,
        name: str = "int_dvf",
        **kwargs,
    ):
        """
        Init.

        :param fixed_image_size: tuple, (f_dim1, f_dim2, f_dim3)
        :param num_steps: int, number of steps for integration
        :param name: name of the layer
        :param kwargs: additional arguments.
        """
        super().__init__(name=name, **kwargs)
        assert len(fixed_image_size) == 3
        self._fixed_image_size = fixed_image_size
        self._num_steps = num_steps
        self._warping = Warping(fixed_image_size=fixed_image_size)

    def call(self, inputs: tf.Tensor, **kwargs) -> tf.Tensor:
        """
        :param inputs: dvf, shape = (batch, f_dim1, f_dim2, f_dim3, 3)
        :param kwargs: additional arguments.
        :return: ddf, shape = (batch, f_dim1, f_dim2, f_dim3, 3)
        """
        ddf = inputs / (2 ** self._num_steps)
        for _ in range(self._num_steps):
            ddf += self._warping(inputs=[ddf, ddf])
        return ddf

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


class ResizeCPTransform(tfkl.Layer):
    """
    Layer for getting the control points from the output of a image-to-image network.
    It uses an anti-aliasing Gaussian filter before downsampling.
    """

    def __init__(self, control_point_spacing: (list, tuple, int), **kwargs):
        """
        :param control_point_spacing: list or int
        :param kwargs: additional arguments.
        """
        super().__init__(**kwargs)

        if isinstance(control_point_spacing, int):
            control_point_spacing = [control_point_spacing] * 3

        self.kernel_sigma = [
            0.44 * cp for cp in control_point_spacing
        ]  # 0.44 = ln(4)/pi
        self.cp_spacing = control_point_spacing
        self.kernel = None
        self._output_shape = None
        self._resize = None

    def build(self, input_shape):
        super().build(input_shape=input_shape)

        self.kernel = layer_util.gaussian_filter_3d(self.kernel_sigma)
        output_shape = [
            tf.cast(tf.math.ceil(v / c) + 3, tf.int32)
            for v, c in zip(input_shape[1:-1], self.cp_spacing)
        ]
        self._output_shape = output_shape
        self._resize = Resize3d(output_shape)

    def call(self, inputs, **kwargs) -> tf.Tensor:
        output = tf.nn.conv3d(
            inputs, self.kernel, strides=(1, 1, 1, 1, 1), padding="SAME"
        )
        output = self._resize(inputs=output)
        return output


class BSplines3DTransform(tfkl.Layer):
    """
     Layer for BSplines interpolation with precomputed cubic spline kernel_size.
     It assumes a full sized image from which:
     1. it compute the contol points values by downsampling the initial image
     2. performs the interpolation
     3. crops the image around the valid values.

    :param cp_spacing: int or tuple of three ints specifying the spacing (in pixels)
        in each dimension. When a single int is used,
        the same spacing to all dimensions is used
    :param output_shape: (batch_size, dim0, dim1, dim2, 3) of the high resolution
        deformation fields.
    :param kwargs: additional arguments.
    """

    def __init__(self, cp_spacing: (int, tuple), output_shape: tuple, **kwargs):

        super().__init__(**kwargs)

        self.filters = []
        self._output_shape = output_shape

        if isinstance(cp_spacing, int):
            self.cp_spacing = (cp_spacing, cp_spacing, cp_spacing)
        else:
            self.cp_spacing = cp_spacing

    def build(self, input_shape: tuple):

        """
        :param input_shape: tuple with the input shape
        :return: None
        """

        super().build(input_shape=input_shape)

        b = {
            0: lambda u: np.float64((1 - u) ** 3 / 6),
            1: lambda u: np.float64((3 * (u ** 3) - 6 * (u ** 2) + 4) / 6),
            2: lambda u: np.float64((-3 * (u ** 3) + 3 * (u ** 2) + 3 * u + 1) / 6),
            3: lambda u: np.float64(u ** 3 / 6),
        }

        filters = np.zeros(
            (
                4 * self.cp_spacing[0],
                4 * self.cp_spacing[1],
                4 * self.cp_spacing[2],
                3,
                3,
            ),
            dtype=np.float32,
        )

        u_arange = 1 - np.arange(
            1 / (2 * self.cp_spacing[0]), 1, 1 / self.cp_spacing[0]
        )
        v_arange = 1 - np.arange(
            1 / (2 * self.cp_spacing[1]), 1, 1 / self.cp_spacing[1]
        )
        w_arange = 1 - np.arange(
            1 / (2 * self.cp_spacing[2]), 1, 1 / self.cp_spacing[2]
        )

        filter_idx = [[0, 1, 2, 3] for _ in range(3)]
        filter_coord = list(itertools.product(*filter_idx))

        for f_idx in filter_coord:
            for it_dim in range(3):
                filters[
                    f_idx[0] * self.cp_spacing[0] : (f_idx[0] + 1) * self.cp_spacing[0],
                    f_idx[1] * self.cp_spacing[1] : (f_idx[1] + 1) * self.cp_spacing[1],
                    f_idx[2] * self.cp_spacing[2] : (f_idx[2] + 1) * self.cp_spacing[2],
                    it_dim,
                    it_dim,
                ] = (
                    b[f_idx[0]](u_arange)[:, None, None]
                    * b[f_idx[1]](v_arange)[None, :, None]
                    * b[f_idx[2]](w_arange)[None, None, :]
                )

        self.filter = tf.convert_to_tensor(filters)

    def interpolate(self, field) -> tf.Tensor:

        """
        :param field: tf.Tensor with shape=number_of_control_points_per_dim
        :return: interpolated_field: tf.Tensor
        """

        image_shape = tuple(
            [(a - 1) * b + 4 * b for a, b in zip(field.shape[1:-1], self.cp_spacing)]
        )

        output_shape = (field.shape[0],) + image_shape + (3,)
        return tf.nn.conv3d_transpose(
            field,
            self.filter,
            output_shape=output_shape,
            strides=self.cp_spacing,
            padding="VALID",
        )

    def call(self, inputs, **kwargs) -> tf.Tensor:

        """
        :param inputs: tf.Tensor defining a low resolution free-form deformation field
        :param kwargs: additional arguments.
        :return: interpolated_field: tf.Tensor of shape=self.input_shape
        """
        high_res_field = self.interpolate(inputs)

        index = [int(3 * c) for c in self.cp_spacing]
        return high_res_field[
            :,
            index[0] : index[0] + self._output_shape[0],
            index[1] : index[1] + self._output_shape[1],
            index[2] : index[2] + self._output_shape[2],
        ]


1			"""This module defines custom layers."""
2			import itertools
3
4			import numpy as np
5			import tensorflow as tf
6			import tensorflow.keras.layers as tfkl
7
8			import deepreg.model.layer_util as layer_util
9
10			LAYER_DICT = dict(conv3d=tfkl.Conv3D, deconv3d=tfkl.Conv3DTranspose)
11			NORM_DICT = dict(batch=tfkl.BatchNormalization, layer=tfkl.LayerNormalization)
12
13
14			class NormBlock(tfkl.Layer):
15			"""
16			A block with layer - norm - activation.
17			"""
18
19			def __init__(
20			self,
21			layer_name: str,
22			norm_name: str = "batch",
23			activation: str = "relu",
24			name: str = "norm_block",
25			**kwargs,
26			):
27			"""
28			Init.
29
30			:param layer_name: class of the layer to be wrapped.
31			:param norm_name: class of the normalization layer.
32			:param activation: name of activation.
33			:param name: name of the block layer.
34			:param kwargs: additional arguments.
35			"""
36			super().__init__()
37			self._config = dict(
38			layer_name=layer_name,
39			norm_name=norm_name,
40			activation=activation,
41			name=name,
42			**kwargs,
43			)
44			self._layer = LAYER_DICT[layer_name](use_bias=False, **kwargs)
45			self._norm = NORM_DICT[norm_name]()
46			self._act = tfkl.Activation(activation=activation)
47
48			def call(self, inputs, training=None, **kwargs) -> tf.Tensor:
			0 ignored issues – show Bug introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Parameters differ from overridden 'call' method Loading history... introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report "inputs, training" missing in parameter type documentation Loading history...
49			"""
50			Forward.
51
52			:param inputs: inputs for the layer
53			:param training: training flag for normalization layers (default: None)
54			:param kwargs: additional arguments.
55			:return:
56			"""
57			output = self._layer(inputs=inputs)
58			output = self._norm(inputs=output, training=training)
59			output = self._act(output)
60			return output
61
62			def get_config(self) -> dict:
63			"""Return the config dictionary for recreating this class."""
64			config = super().get_config()
65			config.update(self._config)
66			return config
67
68
69			class Conv3dBlock(NormBlock):
70			"""
71			A conv3d block having conv3d - norm - activation.
72			"""
73
74			def __init__(
75			self,
76			name: str = "conv3d_block",
77			**kwargs,
78			):
79			"""
80			Init.
81
82			:param name: name of the layer
83			:param kwargs: additional arguments.
84			"""
85			super().__init__(layer_name="conv3d", name=name, **kwargs)
86
87
88			class Deconv3dBlock(NormBlock):
89			"""
90			A deconv3d block having conv3d - norm - activation.
91			"""
92
93			def __init__(
94			self,
95			name: str = "deconv3d_block",
96			**kwargs,
97			):
98			"""
99			Init.
100
101			:param name: name of the layer
102			:param kwargs: additional arguments.
103			"""
104			super().__init__(layer_name="deconv3d", name=name, **kwargs)
105
106
107			class Resize3d(tfkl.Layer):
108			"""
109			Resize image in two folds.
110
111			- resize dim2 and dim3
112			- resize dim1 and dim2
113			"""
114
115			def __init__(
116			self,
117			shape: tuple,
118			method: str = tf.image.ResizeMethod.BILINEAR,
119			name: str = "resize3d",
120			):
121			"""
122			Init, save arguments.
123
124			:param shape: (dim1, dim2, dim3)
125			:param method: tf.image.ResizeMethod
126			:param name: name of the layer
127			"""
128			super().__init__(name=name)
129			assert len(shape) == 3
130			self._shape = shape
131			self._method = method
132
133			def call(self, inputs: tf.Tensor, **kwargs) -> tf.Tensor:
			0 ignored issues – show introduced 2021-01-30 23:31 UTC by Report Bug Copy Issue Report "ValueError" not documented as being raised Loading history...
134			"""
135			Perform two fold resize.
136
137			:param inputs: shape = (batch, dim1, dim2, dim3, channels)
138			or (batch, dim1, dim2, dim3)
139			or (dim1, dim2, dim3)
140			:param kwargs: additional arguments
141			:return: shape = (batch, out_dim1, out_dim2, out_dim3, channels)
142			or (batch, dim1, dim2, dim3)
143			or (dim1, dim2, dim3)
144			"""
145			# sanity check
146			image = inputs
147			image_dim = len(image.shape)
148
149			# init
150			if image_dim == 5:
151			has_channel = True
152			has_batch = True
153			input_image_shape = image.shape[1:4]
154			elif image_dim == 4:
155			has_channel = False
156			has_batch = True
157			input_image_shape = image.shape[1:4]
158			elif image_dim == 3:
159			has_channel = False
160			has_batch = False
161			input_image_shape = image.shape[0:3]
162			else:
163			raise ValueError(
164			"Resize3d takes input image of dimension 3 or 4 or 5, "
165			"corresponding to (dim1, dim2, dim3) "
166			"or (batch, dim1, dim2, dim3) "
167			"or (batch, dim1, dim2, dim3, channels), "
168			"got image shape{}".format(image.shape)
169			)
170
171			# no need of resize
172			if input_image_shape == tuple(self._shape):
173			return image
174
175			# expand to five dimensions
176			if not has_batch:
177			image = tf.expand_dims(image, axis=0)
178			if not has_channel:
179			image = tf.expand_dims(image, axis=-1)
180			assert len(image.shape) == 5 # (batch, dim1, dim2, dim3, channels)
181			image_shape = tf.shape(image)
182
183			# merge axis 0 and 1
184			output = tf.reshape(
185			image, (-1, image_shape[2], image_shape[3], image_shape[4])
186			) # (batch * dim1, dim2, dim3, channels)
187
188			# resize dim2 and dim3
189			output = tf.image.resize(
190			images=output, size=self._shape[1:3], method=self._method
191			) # (batch * dim1, out_dim2, out_dim3, channels)
192
193			# split axis 0 and merge axis 3 and 4
194			output = tf.reshape(
195			output,
196			shape=(-1, image_shape[1], self._shape[1], self._shape[2] * image_shape[4]),
197			) # (batch, dim1, out_dim2, out_dim3 * channels)
198
199			# resize dim1 and dim2
200			output = tf.image.resize(
201			images=output, size=self._shape[:2], method=self._method
202			) # (batch, out_dim1, out_dim2, out_dim3 * channels)
203
204			# reshape
205			output = tf.reshape(
206			output, shape=[-1, *self._shape, image_shape[4]]
207			) # (batch, out_dim1, out_dim2, out_dim3, channels)
208
209			# squeeze to original dimension
210			if not has_batch:
211			output = tf.squeeze(output, axis=0)
212			if not has_channel:
213			output = tf.squeeze(output, axis=-1)
214			return output
215
216			def get_config(self) -> dict:
217			"""Return the config dictionary for recreating this class."""
218			config = super().get_config()
219			config["shape"] = self._shape
220			config["method"] = self._method
221			return config
222
223
224			class Warping(tfkl.Layer):
225			"""
226			Warps an image with DDF.
227
228			Reference:
229
230			https://github.com/adalca/neurite/blob/legacy/neuron/utils.py
231			where vol = image, loc_shift = ddf
232			"""
233
234			def __init__(self, fixed_image_size: tuple, name: str = "warping", **kwargs):
235			"""
236			Init.
237
238			:param fixed_image_size: shape = (f_dim1, f_dim2, f_dim3)
239			or (f_dim1, f_dim2, f_dim3, ch) with the last channel for features
240			:param name: name of the layer
241			:param kwargs: additional arguments.
242			"""
243			super().__init__(name=name, **kwargs)
244			self._fixed_image_size = fixed_image_size
245			# shape = (1, f_dim1, f_dim2, f_dim3, 3)
246			self.grid_ref = layer_util.get_reference_grid(grid_size=fixed_image_size)
247			self.grid_ref = self.grid_ref[None, ...]
248
249			def call(self, inputs, **kwargs) -> tf.Tensor:
			0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report "inputs" missing in parameter type documentation Loading history...
250			"""
251			:param inputs: (ddf, image)
252
253			- ddf, shape = (batch, f_dim1, f_dim2, f_dim3, 3)
254			- image, shape = (batch, m_dim1, m_dim2, m_dim3)
255			:param kwargs: additional arguments.
256			:return: shape = (batch, f_dim1, f_dim2, f_dim3)
257			"""
258			ddf, image = inputs
259			return layer_util.resample(vol=image, loc=self.grid_ref + ddf)
260
261			def get_config(self) -> dict:
262			"""Return the config dictionary for recreating this class."""
263			config = super().get_config()
264			config["fixed_image_size"] = self._fixed_image_size
265			return config
266
267
268			class ResidualBlock(tfkl.Layer):
269			"""
270			A block with skip links and layer - norm - activation.
271			"""
272
273			def __init__(
274			self,
275			layer_name: str,
276			num_layers: int = 2,
277			norm_name: str = "batch",
278			activation: str = "relu",
279			name: str = "res_block",
280			**kwargs,
281			):
282			"""
283			Init.
284
285			:param layer_name: class of the layer to be wrapped.
286			:param num_layers: number of layers/blocks.
287			:param norm_name: class of the normalization layer.
288			:param activation: name of activation.
289			:param name: name of the block layer.
290			:param kwargs: additional arguments.
291			"""
292			super().__init__()
293			self._num_layers = num_layers
294			self._config = dict(
295			layer_name=layer_name,
296			num_layers=num_layers,
297			norm_name=norm_name,
298			activation=activation,
299			name=name,
300			**kwargs,
301			)
302			self._layers = [
303			LAYER_DICT[layer_name](use_bias=False, **kwargs) for _ in range(num_layers)
304			]
305			self._norms = [NORM_DICT[norm_name]() for _ in range(num_layers)]
306			self._acts = [tfkl.Activation(activation=activation) for _ in range(num_layers)]
307
308			def call(self, inputs, training=None, **kwargs) -> tf.Tensor:
			0 ignored issues – show Bug introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Parameters differ from overridden 'call' method Loading history... introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report "inputs, training" missing in parameter type documentation Loading history...
309			"""
310			Forward.
311
312			:param inputs: inputs for the layer
313			:param training: training flag for normalization layers (default: None)
314			:param kwargs: additional arguments.
315			:return:
316			"""
317
318			output = inputs
319			for i in range(self._num_layers):
320			output = self._layers[i](inputs=output)
321			output = self._norms[i](inputs=output, training=training)
322			if i == self._num_layers - 1:
323			# last block
324			output = output + inputs
325			output = self._acts[i](output)
326			return output
327
328			def get_config(self) -> dict:
329			"""Return the config dictionary for recreating this class."""
330			config = super().get_config()
331			config.update(self._config)
332			return config
333
334
335			class ResidualConv3dBlock(ResidualBlock):
336			"""
337			A conv3d residual block
338			"""
339
340			def __init__(
341			self,
342			name: str = "conv3d_res_block",
343			**kwargs,
344			):
345			"""
346			Init.
347
348			:param name: name of the layer
349			:param kwargs: additional arguments.
350			"""
351			super().__init__(layer_name="conv3d", name=name, **kwargs)
352
353
354			class IntDVF(tfkl.Layer):
355			"""
356			Integrate DVF to get DDF.
357
358			Reference:
359
360			- integrate_vec of neuron
361			https://github.com/adalca/neurite/blob/legacy/neuron/utils.py
362			"""
363
364			def __init__(
365			self,
366			fixed_image_size: tuple,
367			num_steps: int = 7,
368			name: str = "int_dvf",
369			**kwargs,
370			):
371			"""
372			Init.
373
374			:param fixed_image_size: tuple, (f_dim1, f_dim2, f_dim3)
375			:param num_steps: int, number of steps for integration
376			:param name: name of the layer
377			:param kwargs: additional arguments.
378			"""
379			super().__init__(name=name, **kwargs)
380			assert len(fixed_image_size) == 3
381			self._fixed_image_size = fixed_image_size
382			self._num_steps = num_steps
383			self._warping = Warping(fixed_image_size=fixed_image_size)
384
385			def call(self, inputs: tf.Tensor, **kwargs) -> tf.Tensor:
386			"""
387			:param inputs: dvf, shape = (batch, f_dim1, f_dim2, f_dim3, 3)
388			:param kwargs: additional arguments.
389			:return: ddf, shape = (batch, f_dim1, f_dim2, f_dim3, 3)
390			"""
391			ddf = inputs / (2 ** self._num_steps)
392			for _ in range(self._num_steps):
393			ddf += self._warping(inputs=[ddf, ddf])
394			return ddf
395
396			def get_config(self) -> dict:
397			"""Return the config dictionary for recreating this class."""
398			config = super().get_config()
399			config["fixed_image_size"] = self._fixed_image_size
400			config["num_steps"] = self._num_steps
401			return config
402
403
404			class ResizeCPTransform(tfkl.Layer):
405			"""
406			Layer for getting the control points from the output of a image-to-image network.
407			It uses an anti-aliasing Gaussian filter before downsampling.
408			"""
409
410			def __init__(self, control_point_spacing: (list, tuple, int), **kwargs):
411			"""
412			:param control_point_spacing: list or int
413			:param kwargs: additional arguments.
414			"""
415			super().__init__(**kwargs)
416
417			if isinstance(control_point_spacing, int):
418			control_point_spacing = [control_point_spacing] * 3
419
420			self.kernel_sigma = [
421			0.44 * cp for cp in control_point_spacing
422			] # 0.44 = ln(4)/pi
423			self.cp_spacing = control_point_spacing
424			self.kernel = None
425			self._output_shape = None
426			self._resize = None
427
428			def build(self, input_shape):
429			super().build(input_shape=input_shape)
430
431			self.kernel = layer_util.gaussian_filter_3d(self.kernel_sigma)
432			output_shape = [
433			tf.cast(tf.math.ceil(v / c) + 3, tf.int32)
434			for v, c in zip(input_shape[1:-1], self.cp_spacing)
435			]
436			self._output_shape = output_shape
437			self._resize = Resize3d(output_shape)
438
439			def call(self, inputs, **kwargs) -> tf.Tensor:
440			output = tf.nn.conv3d(
441			inputs, self.kernel, strides=(1, 1, 1, 1, 1), padding="SAME"
442			)
443			output = self._resize(inputs=output)
444			return output
445
446
447			class BSplines3DTransform(tfkl.Layer):
448			"""
449			Layer for BSplines interpolation with precomputed cubic spline kernel_size.
450			It assumes a full sized image from which:
451			1. it compute the contol points values by downsampling the initial image
452			2. performs the interpolation
453			3. crops the image around the valid values.
454
455			:param cp_spacing: int or tuple of three ints specifying the spacing (in pixels)
456			in each dimension. When a single int is used,
457			the same spacing to all dimensions is used
458			:param output_shape: (batch_size, dim0, dim1, dim2, 3) of the high resolution
459			deformation fields.
460			:param kwargs: additional arguments.
461			"""
462
463			def __init__(self, cp_spacing: (int, tuple), output_shape: tuple, **kwargs):
464
465			super().__init__(**kwargs)
466
467			self.filters = []
468			self._output_shape = output_shape
469
470			if isinstance(cp_spacing, int):
471			self.cp_spacing = (cp_spacing, cp_spacing, cp_spacing)
472			else:
473			self.cp_spacing = cp_spacing
474
475			def build(self, input_shape: tuple):
			0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Redundant returns documentation Loading history...
476			"""
477			:param input_shape: tuple with the input shape
478			:return: None
479			"""
480
481			super().build(input_shape=input_shape)
482
483			b = {
484			0: lambda u: np.float64((1 - u) ** 3 / 6),
485			1: lambda u: np.float64((3 * (u ** 3) - 6 * (u ** 2) + 4) / 6),
486			2: lambda u: np.float64((-3 * (u ** 3) + 3 * (u ** 2) + 3 * u + 1) / 6),
487			3: lambda u: np.float64(u ** 3 / 6),
488			}
489
490			filters = np.zeros(
491			(
492			4 * self.cp_spacing[0],
493			4 * self.cp_spacing[1],
494			4 * self.cp_spacing[2],
495			3,
496			3,
497			),
498			dtype=np.float32,
499			)
500
501			u_arange = 1 - np.arange(
502			1 / (2 * self.cp_spacing[0]), 1, 1 / self.cp_spacing[0]
503			)
504			v_arange = 1 - np.arange(
505			1 / (2 * self.cp_spacing[1]), 1, 1 / self.cp_spacing[1]
506			)
507			w_arange = 1 - np.arange(
508			1 / (2 * self.cp_spacing[2]), 1, 1 / self.cp_spacing[2]
509			)
510
511			filter_idx = [[0, 1, 2, 3] for _ in range(3)]
512			filter_coord = list(itertools.product(*filter_idx))
513
514			for f_idx in filter_coord:
515			for it_dim in range(3):
516			filters[
517			f_idx[0] * self.cp_spacing[0] : (f_idx[0] + 1) * self.cp_spacing[0],
518			f_idx[1] * self.cp_spacing[1] : (f_idx[1] + 1) * self.cp_spacing[1],
519			f_idx[2] * self.cp_spacing[2] : (f_idx[2] + 1) * self.cp_spacing[2],
520			it_dim,
521			it_dim,
522			] = (
523			b[f_idx[0]](u_arange)[:, None, None]
524			* b[f_idx[1]](v_arange)[None, :, None]
525			* b[f_idx[2]](w_arange)[None, None, :]
526			)
527
528			self.filter = tf.convert_to_tensor(filters)
529
530			def interpolate(self, field) -> tf.Tensor:
			0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report "field" missing in parameter type documentation Loading history...
531			"""
532			:param field: tf.Tensor with shape=number_of_control_points_per_dim
533			:return: interpolated_field: tf.Tensor
534			"""
535
536			image_shape = tuple(
537			[(a - 1) * b + 4 * b for a, b in zip(field.shape[1:-1], self.cp_spacing)]
538			)
539
540			output_shape = (field.shape[0],) + image_shape + (3,)
541			return tf.nn.conv3d_transpose(
542			field,
543			self.filter,
544			output_shape=output_shape,
545			strides=self.cp_spacing,
546			padding="VALID",
547			)
548
549			def call(self, inputs, **kwargs) -> tf.Tensor:
			0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report "inputs" missing in parameter type documentation Loading history...
550			"""
551			:param inputs: tf.Tensor defining a low resolution free-form deformation field
552			:param kwargs: additional arguments.
553			:return: interpolated_field: tf.Tensor of shape=self.input_shape
554			"""
555			high_res_field = self.interpolate(inputs)
556
557			index = [int(3 * c) for c in self.cp_spacing]
558			return high_res_field[
559			:,
560			index[0] : index[0] + self._output_shape[0],
561			index[1] : index[1] + self._output_shape[1],
562			index[2] : index[2] + self._output_shape[2],
563			]
564

DeepRegNet / DeepReg

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deepreg.model.layer.Deconv3d.__init__() A

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