deepreg.model.layer_util.resize3d() - 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 2021-01-30 23:28 UTC

deepreg.model.layer_util.resize3d() C

↳ Parent: Project

Complexity

Conditions

Size

Total Lines	88
Code Lines	43

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	43
dl	0
loc	88
rs	5.9999
c	0
b	0
f	0
cc	10
nop	3

How to fix Long Method Complexity

"""
Module containing utilities for layer inputs
"""
import itertools

import numpy as np
import tensorflow as tf


def get_reference_grid(grid_size: (tuple, list)) -> tf.Tensor:
    """
    Generate a 3D grid with given size.

    Reference:

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

      neuron modifies meshgrid to make it faster, however local
      benchmark suggests tf.meshgrid is better

    Note:

    for tf.meshgrid, in the 3-D case with inputs of length M, N and P,
    outputs are of shape (N, M, P) for ‘xy’ indexing and
    (M, N, P) for ‘ij’ indexing.

    :param grid_size: list or tuple of size 3, [dim1, dim2, dim3]
    :return: shape = (dim1, dim2, dim3, 3),
             grid[i, j, k, :] = [i j k]
    """

    # dim1, dim2, dim3 = grid_size
    # mesh_grid has three elements, corresponding to i, j, k
    # for i in range(dim1)
    #     for j in range(dim2)
    #         for k in range(dim3)
    #             mesh_grid[0][i,j,k] = i
    #             mesh_grid[1][i,j,k] = j
    #             mesh_grid[2][i,j,k] = k
    mesh_grid = tf.meshgrid(
        tf.range(grid_size[0]),
        tf.range(grid_size[1]),
        tf.range(grid_size[2]),
        indexing="ij",
    )  # has three elements, each shape = (dim1, dim2, dim3)
    grid = tf.stack(mesh_grid, axis=3)  # shape = (dim1, dim2, dim3, 3)
    grid = tf.cast(grid, dtype=tf.float32)
    return grid


def get_n_bits_combinations(num_bits: int) -> list:
    """
    Function returning list containing all combinations of n bits.
    Given num_bits binary bits, each bit has value 0 or 1,
    there are in total 2**n_bits combinations.

    :param num_bits: int, number of combinations to evaluate
    :return: a list of length 2**n_bits,
      return[i] is the binary representation of the decimal integer.

    :Example:
        >>> from deepreg.model.layer_util import get_n_bits_combinations
        >>> get_n_bits_combinations(3)
        [[0, 0, 0], # 0
         [0, 0, 1], # 1
         [0, 1, 0], # 2
         [0, 1, 1], # 3
         [1, 0, 0], # 4
         [1, 0, 1], # 5
         [1, 1, 0], # 6
         [1, 1, 1]] # 7
    """
    assert num_bits >= 1
    return [list(i) for i in itertools.product([0, 1], repeat=num_bits)]


def pyramid_combination(

    values: list, weight_floor: list, weight_ceil: list
) -> tf.Tensor:
    r"""
    Calculates linear interpolation (a weighted sum) using values of
    hypercube corners in dimension n.

    For example, when num_dimension = len(loc_shape) = num_bits = 3
    values correspond to values at corners of following coordinates

    .. code-block:: python

        [[0, 0, 0], # even
         [0, 0, 1], # odd
         [0, 1, 0], # even
         [0, 1, 1], # odd
         [1, 0, 0], # even
         [1, 0, 1], # odd
         [1, 1, 0], # even
         [1, 1, 1]] # odd

    values[::2] correspond to the corners with last coordinate == 0

    .. code-block:: python

        [[0, 0, 0],
         [0, 1, 0],
         [1, 0, 0],
         [1, 1, 0]]

    values[1::2] correspond to the corners with last coordinate == 1

    .. code-block:: python

        [[0, 0, 1],
         [0, 1, 1],
         [1, 0, 1],
         [1, 1, 1]]

    The weights correspond to the floor corners.
    For example, when num_dimension = len(loc_shape) = num_bits = 3,
    weight_floor = [f1, f2, f3] (ignoring the batch dimension).
    weight_ceil = [c1, c2, c3] (ignoring the batch dimension).

    So for corner with coords (x, y, z), x, y, z's values are 0 or 1

    - weight for x = f1 if x = 0 else c1
    - weight for y = f2 if y = 0 else c2
    - weight for z = f3 if z = 0 else c3

    so the weight for (x, y, z) is

    .. code-block:: text

        W_xyz = ((1-x) * f1 + x * c1)
              * ((1-y) * f2 + y * c2)
              * ((1-z) * f3 + z * c3)

    Let

    .. code-block:: text

        W_xy = ((1-x) * f1 + x * c1)
             * ((1-y) * f2 + y * c2)

    Then

    - W_xy0 = W_xy * f3
    - W_xy1 = W_xy * c3

    Similar to W_xyz, denote V_xyz the value at (x, y, z),
    the final sum V equals

    .. code-block:: text

          sum over x,y,z (V_xyz * W_xyz)
        = sum over x,y (V_xy0 * W_xy0 + V_xy1 * W_xy1)
        = sum over x,y (V_xy0 * W_xy * f3 + V_xy1 * W_xy * c3)
        = sum over x,y (V_xy0 * W_xy) * f3 + sum over x,y (V_xy1 * W_xy) * c3

    That's why we call this pyramid combination.
    It calculates the linear interpolation gradually, starting from
    the last dimension.
    The key is that the weight of each corner is the product of the weights
    along each dimension.

    :param values: a list having values on the corner,
                   it has 2**n tensors of shape
                   (\*loc_shape) or (batch, \*loc_shape) or (batch, \*loc_shape, ch)
                   the order is consistent with get_n_bits_combinations
                   loc_shape is independent from n, aka num_dim
    :param weight_floor: a list having weights of floor points,
                    it has n tensors of shape
                    (\*loc_shape) or (batch, \*loc_shape) or (batch, \*loc_shape, 1)
    :param weight_ceil: a list having weights of ceil points,
                    it has n tensors of shape
                    (\*loc_shape) or (batch, \*loc_shape) or (batch, \*loc_shape, 1)
    :return: one tensor of the same shape as an element in values
             (\*loc_shape) or (batch, \*loc_shape) or (batch, \*loc_shape, 1)
    """
    v_shape = values[0].shape
    wf_shape = weight_floor[0].shape
    wc_shape = weight_ceil[0].shape
    if len(v_shape) != len(wf_shape) or len(v_shape) != len(wc_shape):
        raise ValueError(
            "In pyramid_combination, elements of "
            "values, weight_floor, and weight_ceil should have same dimension. "
            f"value shape = {v_shape}, "
            f"weight_floor = {wf_shape}, "
            f"weight_ceil = {wc_shape}."
        )
    if 2 ** len(weight_floor) != len(values):
        raise ValueError(
            "In pyramid_combination, "
            "num_dim = len(weight_floor), "
            "len(values) must be 2 ** num_dim, "
            f"But len(weight_floor) = {len(weight_floor)}, "
            f"len(values) = {len(values)}"
        )

    if len(weight_floor) == 1:  # one dimension
        return values[0] * weight_floor[0] + values[1] * weight_ceil[0]
    # multi dimension
    values_floor = pyramid_combination(
        values=values[::2],
        weight_floor=weight_floor[:-1],
        weight_ceil=weight_ceil[:-1],
    )
    values_floor = values_floor * weight_floor[-1]
    values_ceil = pyramid_combination(
        values=values[1::2],
        weight_floor=weight_floor[:-1],
        weight_ceil=weight_ceil[:-1],
    )
    values_ceil = values_ceil * weight_ceil[-1]
    return values_floor + values_ceil


def resample(

    vol: tf.Tensor,
    loc: tf.Tensor,
    interpolation: str = "linear",
    zero_boundary: bool = True,
) -> tf.Tensor:
    r"""
    Sample the volume at given locations.

    Input has

    - volume, vol, of shape = (batch, v_dim 1, ..., v_dim n),
      or (batch, v_dim 1, ..., v_dim n, ch),
      where n is the dimension of volume,
      ch is the extra dimension as features.

      Denote vol_shape = (v_dim 1, ..., v_dim n)

    - location, loc, of shape = (batch, l_dim 1, ..., l_dim m, n),
      where m is the dimension of output.

      Denote loc_shape = (l_dim 1, ..., l_dim m)

    Reference:

    - neuron's interpn
      https://github.com/adalca/neurite/blob/legacy/neuron/utils.py

      Difference

      1. they dont have batch size
      2. they support more dimensions in vol

      TODO try not using stack as neuron claims it's slower

    :param vol: shape = (batch, \*vol_shape) or (batch, \*vol_shape, ch)
      with the last channel for features
    :param loc: shape = (batch, \*loc_shape, n)
      such that loc[b, l1, ..., lm, :] = [v1, ..., vn] is of shape (n,),
      which represents a point in vol, with coordinates (v1, ..., vn)
    :param interpolation: linear only, TODO support nearest
    :param zero_boundary: if true, values on or outside boundary will be zeros
    :return: shape = (batch, \*loc_shape) or (batch, \*loc_shape, ch)
    """

    if interpolation != "linear":
        raise ValueError("resample supports only linear interpolation")

    # init
    batch_size = vol.shape[0]
    loc_shape = loc.shape[1:-1]
    dim_vol = loc.shape[-1]  # dimension of vol, n
    if dim_vol == len(vol.shape) - 1:
        # vol.shape = (batch, *vol_shape)
        has_ch = False
    elif dim_vol == len(vol.shape) - 2:
        # vol.shape = (batch, *vol_shape, ch)
        has_ch = True
    else:
        raise ValueError(
            "vol shape inconsistent with loc "
            "vol.shape = {}, loc.shape = {}".format(vol.shape, loc.shape)
        )
    vol_shape = vol.shape[1 : dim_vol + 1]

    # get floor/ceil for loc and stack, then clip together
    # loc, loc_floor, loc_ceil are have shape (batch, *loc_shape, n)
    loc_ceil = tf.math.ceil(loc)
    loc_floor = loc_ceil - 1
    # (batch, *loc_shape, n, 3)
    clipped = tf.stack([loc, loc_floor, loc_ceil], axis=-1)
    clip_value_max = tf.cast(vol_shape, dtype=clipped.dtype) - 1  # (n,)
    clipped_shape = [1] * (len(loc_shape) + 1) + [dim_vol, 1]
    clip_value_max = tf.reshape(clip_value_max, shape=clipped_shape)
    clipped = tf.clip_by_value(clipped, clip_value_min=0, clip_value_max=clip_value_max)

    # loc_floor_ceil has n sublists
    # each one corresponds to the floor and ceil coordinates for d-th dimension
    # each tensor is of shape (batch, *loc_shape), dtype int32

    # weight_floor has n tensors
    # each tensor is the weight for the corner of floor coordinates
    # each tensor's shape is (batch, *loc_shape) if volume has no feature channel
    #                        (batch, *loc_shape, 1) if volume has feature channel
    loc_floor_ceil, weight_floor, weight_ceil = [], [], []
    # using for loop is faster than using list comprehension
    for dim in range(dim_vol):
        # shape = (batch, *loc_shape)
        c_clipped = clipped[..., dim, 0]
        c_floor = clipped[..., dim, 1]
        c_ceil = clipped[..., dim, 2]
        w_floor = c_ceil - c_clipped  # shape = (batch, *loc_shape)
        w_ceil = c_clipped - c_floor if zero_boundary else 1 - w_floor
        if has_ch:
            w_floor = tf.expand_dims(w_floor, -1)  # shape = (batch, *loc_shape, 1)
            w_ceil = tf.expand_dims(w_ceil, -1)  # shape = (batch, *loc_shape, 1)

        loc_floor_ceil.append([tf.cast(c_floor, tf.int32), tf.cast(c_ceil, tf.int32)])
        weight_floor.append(w_floor)
        weight_ceil.append(w_ceil)

    # 2**n corners, each is a list of n binary values
    corner_indices = get_n_bits_combinations(num_bits=len(vol_shape))

    # batch_coords[b, l1, ..., lm] = b
    # range(batch_size) on axis 0 and repeated on other axes
    # add batch coords manually is faster than using batch_dims in tf.gather_nd
    batch_coords = tf.tile(
        tf.reshape(tf.range(batch_size), [batch_size] + [1] * len(loc_shape)),
        [1] + loc_shape,
    )  # shape = (batch, *loc_shape)

    # get vol values on n-dim hypercube corners
    # corner_values has 2 ** n elements
    # each of shape (batch, *loc_shape) or (batch, *loc_shape, ch)
    corner_values = [
        tf.gather_nd(
            vol,  # shape = (batch, *vol_shape) or (batch, *vol_shape, ch)
            tf.stack(
                [batch_coords]
                + [loc_floor_ceil[axis][fc_idx] for axis, fc_idx in enumerate(c)],
                axis=-1,
            ),  # shape = (batch, *loc_shape, n+1) after stack
        )
        for c in corner_indices  # c is list of len n
    ]  # each tensor has shape (batch, *loc_shape) or (batch, *loc_shape, ch)

    # resample
    sampled = pyramid_combination(
        values=corner_values, weight_floor=weight_floor, weight_ceil=weight_ceil
    )
    return sampled


def warp_grid(grid: tf.Tensor, theta: tf.Tensor) -> tf.Tensor:
    """
    Perform transformation on the grid.

    - grid_padded[i,j,k,:] = [i j k 1]
    - grid_warped[b,i,j,k,p] = sum_over_q (grid_padded[i,j,k,q] * theta[b,q,p])

    :param grid: shape = (dim1, dim2, dim3, 3), grid[i,j,k,:] = [i j k]
    :param theta: parameters of transformation, shape = (batch, 4, 3)
    :return: shape = (batch, dim1, dim2, dim3, 3)
    """

    # grid_padded[i,j,k,:] = [i j k 1], shape = (dim1, dim2, dim3, 4)
    grid_padded = tf.concat([grid, tf.ones_like(grid[..., :1])], axis=3)

    # grid_warped[b,i,j,k,p] = sum_over_q (grid_padded[i,j,k,q] * theta[b,q,p])
    # shape = (batch, dim1, dim2, dim3, 3)
    grid_warped = tf.einsum("ijkq,bqp->bijkp", grid_padded, theta)
    return grid_warped


def gaussian_filter_3d(kernel_sigma: (list, tuple, int)) -> tf.Tensor:
    """
    Define a gaussian filter in 3d for smoothing.

    The filter size is defined 3*kernel_sigma


    :param kernel_sigma: the deviation at each direction (list)
        or use an isotropic deviation (int)
    :return: kernel: tf.Tensor specify a gaussian kernel of shape:
        [3*k for k in kernel_sigma]
    """
    if isinstance(kernel_sigma, int):
        kernel_sigma = (kernel_sigma, kernel_sigma, kernel_sigma)

    kernel_size = [
        int(np.ceil(ks * 3) + np.mod(np.ceil(ks * 3) + 1, 2)) for ks in kernel_sigma
    ]

    # Create a x, y coordinate grid of shape (kernel_size, kernel_size, 2)
    coord = [np.arange(ks) for ks in kernel_size]

    xx, yy, zz = np.meshgrid(coord[0], coord[1], coord[2], indexing="ij")
    xyz_grid = np.concatenate(
        (xx[np.newaxis], yy[np.newaxis], zz[np.newaxis]), axis=0
    )  # 2, y, x

    mean = np.asarray([(ks - 1) / 2.0 for ks in kernel_size])
    mean = mean.reshape(-1, 1, 1, 1)
    variance = np.asarray([ks ** 2.0 for ks in kernel_sigma])
    variance = variance.reshape(-1, 1, 1, 1)

    # Calculate the 2-dimensional gaussian kernel which is
    # the product of two gaussian distributions for two different
    # variables (in this case called x and y)
    # 2.506628274631 = sqrt(2 * pi)

    norm_kernel = 1.0 / (np.sqrt(2 * np.pi) ** 3 + np.prod(kernel_sigma))
    kernel = norm_kernel * np.exp(
        -np.sum((xyz_grid - mean) ** 2.0 / (2 * variance), axis=0)
    )

    # Make sure sum of values in gaussian kernel equals 1.
    kernel = kernel / np.sum(kernel)

    # Reshape
    kernel = kernel.reshape(kernel_size[0], kernel_size[1], kernel_size[2])

    # Total kernel
    total_kernel = np.zeros(tuple(kernel_size) + (3, 3))
    total_kernel[..., 0, 0] = kernel
    total_kernel[..., 1, 1] = kernel
    total_kernel[..., 2, 2] = kernel

    return tf.convert_to_tensor(total_kernel, dtype=tf.float32)


1			"""
2			Module containing utilities for layer inputs
3			"""
4			import itertools
5
6			import numpy as np
7			import tensorflow as tf
8
9
10			def get_reference_grid(grid_size: (tuple, list)) -> tf.Tensor:
11			"""
12			Generate a 3D grid with given size.
13
14			Reference:
15
16			- volshape_to_meshgrid of neuron
17			https://github.com/adalca/neurite/blob/legacy/neuron/utils.py
18
19			neuron modifies meshgrid to make it faster, however local
20			benchmark suggests tf.meshgrid is better
21
22			Note:
23
24			for tf.meshgrid, in the 3-D case with inputs of length M, N and P,
25			outputs are of shape (N, M, P) for ‘xy’ indexing and
26			(M, N, P) for ‘ij’ indexing.
27
28			:param grid_size: list or tuple of size 3, [dim1, dim2, dim3]
29			:return: shape = (dim1, dim2, dim3, 3),
30			grid[i, j, k, :] = [i j k]
31			"""
32
33			# dim1, dim2, dim3 = grid_size
34			# mesh_grid has three elements, corresponding to i, j, k
35			# for i in range(dim1)
36			# for j in range(dim2)
37			# for k in range(dim3)
38			# mesh_grid[0][i,j,k] = i
39			# mesh_grid[1][i,j,k] = j
40			# mesh_grid[2][i,j,k] = k
41			mesh_grid = tf.meshgrid(
42			tf.range(grid_size[0]),
43			tf.range(grid_size[1]),
44			tf.range(grid_size[2]),
45			indexing="ij",
46			) # has three elements, each shape = (dim1, dim2, dim3)
47			grid = tf.stack(mesh_grid, axis=3) # shape = (dim1, dim2, dim3, 3)
48			grid = tf.cast(grid, dtype=tf.float32)
49			return grid
50
51
52			def get_n_bits_combinations(num_bits: int) -> list:
53			"""
54			Function returning list containing all combinations of n bits.
55			Given num_bits binary bits, each bit has value 0 or 1,
56			there are in total 2**n_bits combinations.
57
58			:param num_bits: int, number of combinations to evaluate
59			:return: a list of length 2**n_bits,
60			return[i] is the binary representation of the decimal integer.
61
62			:Example:
63			>>> from deepreg.model.layer_util import get_n_bits_combinations
64			>>> get_n_bits_combinations(3)
65			[[0, 0, 0], # 0
66			[0, 0, 1], # 1
67			[0, 1, 0], # 2
68			[0, 1, 1], # 3
69			[1, 0, 0], # 4
70			[1, 0, 1], # 5
71			[1, 1, 0], # 6
72			[1, 1, 1]] # 7
73			"""
74			assert num_bits >= 1
75			return [list(i) for i in itertools.product([0, 1], repeat=num_bits)]
76
77
78			def pyramid_combination(
			0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report "ValueError" not documented as being raised Loading history...
79			values: list, weight_floor: list, weight_ceil: list
80			) -> tf.Tensor:
81			r"""
82			Calculates linear interpolation (a weighted sum) using values of
83			hypercube corners in dimension n.
84
85			For example, when num_dimension = len(loc_shape) = num_bits = 3
86			values correspond to values at corners of following coordinates
87
88			.. code-block:: python
89
90			[[0, 0, 0], # even
91			[0, 0, 1], # odd
92			[0, 1, 0], # even
93			[0, 1, 1], # odd
94			[1, 0, 0], # even
95			[1, 0, 1], # odd
96			[1, 1, 0], # even
97			[1, 1, 1]] # odd
98
99			values[::2] correspond to the corners with last coordinate == 0
100
101			.. code-block:: python
102
103			[[0, 0, 0],
104			[0, 1, 0],
105			[1, 0, 0],
106			[1, 1, 0]]
107
108			values[1::2] correspond to the corners with last coordinate == 1
109
110			.. code-block:: python
111
112			[[0, 0, 1],
113			[0, 1, 1],
114			[1, 0, 1],
115			[1, 1, 1]]
116
117			The weights correspond to the floor corners.
118			For example, when num_dimension = len(loc_shape) = num_bits = 3,
119			weight_floor = [f1, f2, f3] (ignoring the batch dimension).
120			weight_ceil = [c1, c2, c3] (ignoring the batch dimension).
121
122			So for corner with coords (x, y, z), x, y, z's values are 0 or 1
123
124			- weight for x = f1 if x = 0 else c1
125			- weight for y = f2 if y = 0 else c2
126			- weight for z = f3 if z = 0 else c3
127
128			so the weight for (x, y, z) is
129
130			.. code-block:: text
131
132			W_xyz = ((1-x) * f1 + x * c1)
133			* ((1-y) * f2 + y * c2)
134			* ((1-z) * f3 + z * c3)
135
136			Let
137
138			.. code-block:: text
139
140			W_xy = ((1-x) * f1 + x * c1)
141			* ((1-y) * f2 + y * c2)
142
143			Then
144
145			- W_xy0 = W_xy * f3
146			- W_xy1 = W_xy * c3
147
148			Similar to W_xyz, denote V_xyz the value at (x, y, z),
149			the final sum V equals
150
151			.. code-block:: text
152
153			sum over x,y,z (V_xyz * W_xyz)
154			= sum over x,y (V_xy0 * W_xy0 + V_xy1 * W_xy1)
155			= sum over x,y (V_xy0 * W_xy * f3 + V_xy1 * W_xy * c3)
156			= sum over x,y (V_xy0 * W_xy) * f3 + sum over x,y (V_xy1 * W_xy) * c3
157
158			That's why we call this pyramid combination.
159			It calculates the linear interpolation gradually, starting from
160			the last dimension.
161			The key is that the weight of each corner is the product of the weights
162			along each dimension.
163
164			:param values: a list having values on the corner,
165			it has 2**n tensors of shape
166			(\loc_shape) or (batch, \loc_shape) or (batch, \*loc_shape, ch)
167			the order is consistent with get_n_bits_combinations
168			loc_shape is independent from n, aka num_dim
169			:param weight_floor: a list having weights of floor points,
170			it has n tensors of shape
171			(\loc_shape) or (batch, \loc_shape) or (batch, \*loc_shape, 1)
172			:param weight_ceil: a list having weights of ceil points,
173			it has n tensors of shape
174			(\loc_shape) or (batch, \loc_shape) or (batch, \*loc_shape, 1)
175			:return: one tensor of the same shape as an element in values
176			(\loc_shape) or (batch, \loc_shape) or (batch, \*loc_shape, 1)
177			"""
178			v_shape = values[0].shape
179			wf_shape = weight_floor[0].shape
180			wc_shape = weight_ceil[0].shape
181			if len(v_shape) != len(wf_shape) or len(v_shape) != len(wc_shape):
182			raise ValueError(
183			"In pyramid_combination, elements of "
184			"values, weight_floor, and weight_ceil should have same dimension. "
185			f"value shape = {v_shape}, "
186			f"weight_floor = {wf_shape}, "
187			f"weight_ceil = {wc_shape}."
188			)
189			if 2 ** len(weight_floor) != len(values):
190			raise ValueError(
191			"In pyramid_combination, "
192			"num_dim = len(weight_floor), "
193			"len(values) must be 2 ** num_dim, "
194			f"But len(weight_floor) = {len(weight_floor)}, "
195			f"len(values) = {len(values)}"
196			)
197
198			if len(weight_floor) == 1: # one dimension
199			return values[0] * weight_floor[0] + values[1] * weight_ceil[0]
200			# multi dimension
201			values_floor = pyramid_combination(
202			values=values[::2],
203			weight_floor=weight_floor[:-1],
204			weight_ceil=weight_ceil[:-1],
205			)
206			values_floor = values_floor * weight_floor[-1]
207			values_ceil = pyramid_combination(
208			values=values[1::2],
209			weight_floor=weight_floor[:-1],
210			weight_ceil=weight_ceil[:-1],
211			)
212			values_ceil = values_ceil * weight_ceil[-1]
213			return values_floor + values_ceil
214
215
216			def resample(
			0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report "ValueError" not documented as being raised Loading history...
217			vol: tf.Tensor,
218			loc: tf.Tensor,
219			interpolation: str = "linear",
220			zero_boundary: bool = True,
221			) -> tf.Tensor:
222			r"""
223			Sample the volume at given locations.
224
225			Input has
226
227			- volume, vol, of shape = (batch, v_dim 1, ..., v_dim n),
228			or (batch, v_dim 1, ..., v_dim n, ch),
229			where n is the dimension of volume,
230			ch is the extra dimension as features.
231
232			Denote vol_shape = (v_dim 1, ..., v_dim n)
233
234			- location, loc, of shape = (batch, l_dim 1, ..., l_dim m, n),
235			where m is the dimension of output.
236
237			Denote loc_shape = (l_dim 1, ..., l_dim m)
238
239			Reference:
240
241			- neuron's interpn
242			https://github.com/adalca/neurite/blob/legacy/neuron/utils.py
243
244			Difference
245
246			1. they dont have batch size
247			2. they support more dimensions in vol
248
249			TODO try not using stack as neuron claims it's slower
250
251			:param vol: shape = (batch, \vol_shape) or (batch, \vol_shape, ch)
252			with the last channel for features
253			:param loc: shape = (batch, \*loc_shape, n)
254			such that loc[b, l1, ..., lm, :] = [v1, ..., vn] is of shape (n,),
255			which represents a point in vol, with coordinates (v1, ..., vn)
256			:param interpolation: linear only, TODO support nearest
257			:param zero_boundary: if true, values on or outside boundary will be zeros
258			:return: shape = (batch, \loc_shape) or (batch, \loc_shape, ch)
259			"""
260
261			if interpolation != "linear":
262			raise ValueError("resample supports only linear interpolation")
263
264			# init
265			batch_size = vol.shape[0]
266			loc_shape = loc.shape[1:-1]
267			dim_vol = loc.shape[-1] # dimension of vol, n
268			if dim_vol == len(vol.shape) - 1:
269			# vol.shape = (batch, *vol_shape)
270			has_ch = False
271			elif dim_vol == len(vol.shape) - 2:
272			# vol.shape = (batch, *vol_shape, ch)
273			has_ch = True
274			else:
275			raise ValueError(
276			"vol shape inconsistent with loc "
277			"vol.shape = {}, loc.shape = {}".format(vol.shape, loc.shape)
278			)
279			vol_shape = vol.shape[1 : dim_vol + 1]
280
281			# get floor/ceil for loc and stack, then clip together
282			# loc, loc_floor, loc_ceil are have shape (batch, *loc_shape, n)
283			loc_ceil = tf.math.ceil(loc)
284			loc_floor = loc_ceil - 1
285			# (batch, *loc_shape, n, 3)
286			clipped = tf.stack([loc, loc_floor, loc_ceil], axis=-1)
287			clip_value_max = tf.cast(vol_shape, dtype=clipped.dtype) - 1 # (n,)
288			clipped_shape = [1] * (len(loc_shape) + 1) + [dim_vol, 1]
289			clip_value_max = tf.reshape(clip_value_max, shape=clipped_shape)
290			clipped = tf.clip_by_value(clipped, clip_value_min=0, clip_value_max=clip_value_max)
291
292			# loc_floor_ceil has n sublists
293			# each one corresponds to the floor and ceil coordinates for d-th dimension
294			# each tensor is of shape (batch, *loc_shape), dtype int32
295
296			# weight_floor has n tensors
297			# each tensor is the weight for the corner of floor coordinates
298			# each tensor's shape is (batch, *loc_shape) if volume has no feature channel
299			# (batch, *loc_shape, 1) if volume has feature channel
300			loc_floor_ceil, weight_floor, weight_ceil = [], [], []
301			# using for loop is faster than using list comprehension
302			for dim in range(dim_vol):
303			# shape = (batch, *loc_shape)
304			c_clipped = clipped[..., dim, 0]
305			c_floor = clipped[..., dim, 1]
306			c_ceil = clipped[..., dim, 2]
307			w_floor = c_ceil - c_clipped # shape = (batch, *loc_shape)
308			w_ceil = c_clipped - c_floor if zero_boundary else 1 - w_floor
309			if has_ch:
310			w_floor = tf.expand_dims(w_floor, -1) # shape = (batch, *loc_shape, 1)
311			w_ceil = tf.expand_dims(w_ceil, -1) # shape = (batch, *loc_shape, 1)
312
313			loc_floor_ceil.append([tf.cast(c_floor, tf.int32), tf.cast(c_ceil, tf.int32)])
314			weight_floor.append(w_floor)
315			weight_ceil.append(w_ceil)
316
317			# 2**n corners, each is a list of n binary values
318			corner_indices = get_n_bits_combinations(num_bits=len(vol_shape))
319
320			# batch_coords[b, l1, ..., lm] = b
321			# range(batch_size) on axis 0 and repeated on other axes
322			# add batch coords manually is faster than using batch_dims in tf.gather_nd
323			batch_coords = tf.tile(
324			tf.reshape(tf.range(batch_size), [batch_size] + [1] * len(loc_shape)),
325			[1] + loc_shape,
326			) # shape = (batch, *loc_shape)
327
328			# get vol values on n-dim hypercube corners
329			# corner_values has 2 ** n elements
330			# each of shape (batch, loc_shape) or (batch, loc_shape, ch)
331			corner_values = [
332			tf.gather_nd(
333			vol, # shape = (batch, vol_shape) or (batch, vol_shape, ch)
334			tf.stack(
335			[batch_coords]
336			+ [loc_floor_ceil[axis][fc_idx] for axis, fc_idx in enumerate(c)],
337			axis=-1,
338			), # shape = (batch, *loc_shape, n+1) after stack
339			)
340			for c in corner_indices # c is list of len n
341			] # each tensor has shape (batch, loc_shape) or (batch, loc_shape, ch)
342
343			# resample
344			sampled = pyramid_combination(
345			values=corner_values, weight_floor=weight_floor, weight_ceil=weight_ceil
346			)
347			return sampled
348
349
350			def warp_grid(grid: tf.Tensor, theta: tf.Tensor) -> tf.Tensor:
351			"""
352			Perform transformation on the grid.
353
354			- grid_padded[i,j,k,:] = [i j k 1]
355			- grid_warped[b,i,j,k,p] = sum_over_q (grid_padded[i,j,k,q] * theta[b,q,p])
356
357			:param grid: shape = (dim1, dim2, dim3, 3), grid[i,j,k,:] = [i j k]
358			:param theta: parameters of transformation, shape = (batch, 4, 3)
359			:return: shape = (batch, dim1, dim2, dim3, 3)
360			"""
361
362			# grid_padded[i,j,k,:] = [i j k 1], shape = (dim1, dim2, dim3, 4)
363			grid_padded = tf.concat([grid, tf.ones_like(grid[..., :1])], axis=3)
364
365			# grid_warped[b,i,j,k,p] = sum_over_q (grid_padded[i,j,k,q] * theta[b,q,p])
366			# shape = (batch, dim1, dim2, dim3, 3)
367			grid_warped = tf.einsum("ijkq,bqp->bijkp", grid_padded, theta)
368			return grid_warped
369
370
371			def gaussian_filter_3d(kernel_sigma: (list, tuple, int)) -> tf.Tensor:
372			"""
373			Define a gaussian filter in 3d for smoothing.
374
375			The filter size is defined 3*kernel_sigma
376
377
378			:param kernel_sigma: the deviation at each direction (list)
379			or use an isotropic deviation (int)
380			:return: kernel: tf.Tensor specify a gaussian kernel of shape:
381			[3*k for k in kernel_sigma]
382			"""
383			if isinstance(kernel_sigma, int):
384			kernel_sigma = (kernel_sigma, kernel_sigma, kernel_sigma)
385
386			kernel_size = [
387			int(np.ceil(ks * 3) + np.mod(np.ceil(ks * 3) + 1, 2)) for ks in kernel_sigma
388			]
389
390			# Create a x, y coordinate grid of shape (kernel_size, kernel_size, 2)
391			coord = [np.arange(ks) for ks in kernel_size]
392
393			xx, yy, zz = np.meshgrid(coord[0], coord[1], coord[2], indexing="ij")
394			xyz_grid = np.concatenate(
395			(xx[np.newaxis], yy[np.newaxis], zz[np.newaxis]), axis=0
396			) # 2, y, x
397
398			mean = np.asarray([(ks - 1) / 2.0 for ks in kernel_size])
399			mean = mean.reshape(-1, 1, 1, 1)
400			variance = np.asarray([ks ** 2.0 for ks in kernel_sigma])
401			variance = variance.reshape(-1, 1, 1, 1)
402
403			# Calculate the 2-dimensional gaussian kernel which is
404			# the product of two gaussian distributions for two different
405			# variables (in this case called x and y)
406			# 2.506628274631 = sqrt(2 * pi)
407
408			norm_kernel = 1.0 / (np.sqrt(2 * np.pi) ** 3 + np.prod(kernel_sigma))
409			kernel = norm_kernel * np.exp(
410			-np.sum((xyz_grid - mean) ** 2.0 / (2 * variance), axis=0)
411			)
412
413			# Make sure sum of values in gaussian kernel equals 1.
414			kernel = kernel / np.sum(kernel)
415
416			# Reshape
417			kernel = kernel.reshape(kernel_size[0], kernel_size[1], kernel_size[2])
418
419			# Total kernel
420			total_kernel = np.zeros(tuple(kernel_size) + (3, 3))
421			total_kernel[..., 0, 0] = kernel
422			total_kernel[..., 1, 1] = kernel
423			total_kernel[..., 2, 2] = kernel
424
425			return tf.convert_to_tensor(total_kernel, dtype=tf.float32)
426

DeepRegNet / DeepReg

Pull Request — main (#656)

deepreg.model.layer_util.resize3d() C

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