test.unit.test_layer_util - Code Metrics - Inspection of "WIP 672 add mypy pre commit hook" - DeepRegNet/DeepReg - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Pull Request — main (#675)

by Yunguan

created 2021-02-25 00:34 UTC

test.unit.test_layer_util A

↳ Parent: Project

Complexity

Total Complexity

Size/Duplication

Total Lines	346
Duplicated Lines	9.25 %

Importance

Changes

Metric	Value
wmc	24
eloc	221
dl	32
loc	346
rs	10
c	0
b	0
f	0

15 Methods

Rating	Name	Duplication	Size	Complexity
A	TestPyramidCombination.test_error_dim()	0	10	2
A	TestLinearResample.test_repeat_extrapolation()	0	15	2
A	TestPyramidCombination.test_error_len()	0	10	2
A	TestGaussianFilter3D.test_kernel_size()	0	14	1
A	TestPyramidCombination.test_2d()	22	22	1
A	TestGaussianFilter3D.test_sum()	0	7	1
A	TestWarpGrid.test_identical()	0	5	1
A	TestPyramidCombination.test_1d()	10	10	1
A	TestLinearResample.test_interpolation_error()	0	7	2
A	TestWarpGrid.test_non_identical()	0	29	1
A	TestLinearResample.test_repeat_zero_bound()	0	23	2
A	TestLinearResample.test_shape_error()	0	6	2
A	TestDeconvOutputPadding.test_1d()	0	37	1
A	TestDeconvOutputPadding.test_n_dim()	0	34	1
A	TestDeconvOutputPadding.test_1d_err()	0	5	2

2 Functions

Rating	Name	Duplication	Size	Complexity
A	test_get_n_bits_combinations()	0	20	1
A	test_get_reference_grid()	0	13	1

How to fix Duplicated Code

"""
Tests for deepreg/model/layer_util.py in
pytest style
"""
from test.unit.util import is_equal_tf
from typing import Tuple, Union

import numpy as np
import pytest
import tensorflow as tf

import deepreg.model.layer_util as layer_util


def test_get_reference_grid():
    """
    Test get_reference_grid by confirming that it generates
    a sample grid test case to is_equal_tf's tolerance level.
    """
    want = tf.constant(
        np.array(
            [[[[0, 0, 0], [0, 0, 1], [0, 0, 2]], [[0, 1, 0], [0, 1, 1], [0, 1, 2]]]],
            dtype=np.float32,
        )
    )
    get = layer_util.get_reference_grid(grid_size=[1, 2, 3])
    assert is_equal_tf(want, get)


def test_get_n_bits_combinations():
    """
    Test get_n_bits_combinations by confirming that it generates
    appropriate solutions for 1D, 2D, and 3D cases.
    """
    # Check n=1 - Pass
    assert layer_util.get_n_bits_combinations(1) == [[0], [1]]
    # Check n=2 - Pass
    assert layer_util.get_n_bits_combinations(2) == [[0, 0], [0, 1], [1, 0], [1, 1]]

    # Check n=3 - Pass
    assert layer_util.get_n_bits_combinations(3) == [
        [0, 0, 0],
        [0, 0, 1],
        [0, 1, 0],
        [0, 1, 1],
        [1, 0, 0],
        [1, 0, 1],
        [1, 1, 0],
        [1, 1, 1],
    ]


class TestPyramidCombination:

    def test_1d(self):

        weights = tf.constant(np.array([[0.2]], dtype=np.float32))
        values = tf.constant(np.array([[1], [2]], dtype=np.float32))

        # expected = 1 * 0.2 + 2 * 2
        expected = tf.constant(np.array([1.8], dtype=np.float32))
        got = layer_util.pyramid_combination(
            values=values, weight_floor=weights, weight_ceil=1 - weights
        )
        assert is_equal_tf(got, expected)

    def test_2d(self):

        weights = tf.constant(np.array([[0.2], [0.3]], dtype=np.float32))
        values = tf.constant(
            np.array(
                [
                    [1],  # value at corner (0, 0), weight = 0.2 * 0.3
                    [2],  # value at corner (0, 1), weight = 0.2 * 0.7
                    [3],  # value at corner (1, 0), weight = 0.8 * 0.3
                    [4],  # value at corner (1, 1), weight = 0.8 * 0.7
                ],
                dtype=np.float32,
            )
        )
        # expected = 1 * 0.2 * 0.3
        #          + 2 * 0.2 * 0.7
        #          + 3 * 0.8 * 0.3
        #          + 4 * 0.8 * 0.7
        expected = tf.constant(np.array([3.3], dtype=np.float32))
        got = layer_util.pyramid_combination(
            values=values, weight_floor=weights, weight_ceil=1 - weights
        )
        assert is_equal_tf(got, expected)

    def test_error_dim(self):

        weights = tf.constant(np.array([[[0.2]], [[0.2]]], dtype=np.float32))
        values = tf.constant(np.array([[1], [2]], dtype=np.float32))
        with pytest.raises(ValueError) as err_info:
            layer_util.pyramid_combination(
                values=values, weight_floor=weights, weight_ceil=1 - weights
            )
        assert (
            "In pyramid_combination, elements of values, weight_floor, "
            "and weight_ceil should have same dimension" in str(err_info.value)
        )

    def test_error_len(self):

        weights = tf.constant(np.array([[0.2]], dtype=np.float32))
        values = tf.constant(np.array([[1]], dtype=np.float32))
        with pytest.raises(ValueError) as err_info:
            layer_util.pyramid_combination(
                values=values, weight_floor=weights, weight_ceil=1 - weights
            )
        assert (
            "In pyramid_combination, num_dim = len(weight_floor), "
            "len(values) must be 2 ** num_dim" in str(err_info.value)
        )


class TestLinearResample:

    x_min, x_max = 0, 2
    y_min, y_max = 0, 2
    # vol are values on grid [0,2]x[0,2]
    # values on each point is 3x+y
    # shape = (1,3,3)
    vol = tf.constant(np.array([[[0, 1, 2], [3, 4, 5], [6, 7, 8]]]), dtype=tf.float32)
    # loc are some points, especially
    # shape = (1,4,3,2)
    loc = tf.constant(
        np.array(
            [
                [
                    [[0, 0], [0, 1], [1, 2]],  # boundary corners
                    [[0.4, 0], [0.5, 2], [2, 1.7]],  # boundary edge
                    [[-0.4, 0.7], [0, 3], [2, 3]],  # outside boundary
                    [[0.4, 0.7], [1, 1], [0.6, 0.3]],  # internal
                ]
            ]
        ),
        dtype=tf.float32,
    )

    @pytest.mark.parametrize("channel", [0, 1, 2])
    def test_repeat_extrapolation(self, channel):

        x = self.loc[..., 0]
        y = self.loc[..., 1]
        x = tf.clip_by_value(x, self.x_min, self.x_max)
        y = tf.clip_by_value(y, self.y_min, self.y_max)
        expected = 3 * x + y

        vol = self.vol
        if channel > 0:
            vol = tf.repeat(vol[..., None], channel, axis=-1)
            expected = tf.repeat(expected[..., None], channel, axis=-1)

        got = layer_util.resample(vol=vol, loc=self.loc, zero_boundary=False)
        assert is_equal_tf(expected, got)

    @pytest.mark.parametrize("channel", [0, 1, 2])
    def test_repeat_zero_bound(self, channel):

        x = self.loc[..., 0]
        y = self.loc[..., 1]
        expected = 3 * x + y
        expected = (
            expected
            * tf.cast(x > self.x_min, tf.float32)
            * tf.cast(x <= self.x_max, tf.float32)
        )
        expected = (
            expected
            * tf.cast(y > self.y_min, tf.float32)
            * tf.cast(y <= self.y_max, tf.float32)
        )

        vol = self.vol
        if channel > 0:
            vol = tf.repeat(vol[..., None], channel, axis=-1)
            expected = tf.repeat(expected[..., None], channel, axis=-1)

        got = layer_util.resample(vol=vol, loc=self.loc, zero_boundary=True)
        assert is_equal_tf(expected, got)

    def test_shape_error(self):

        vol = tf.constant(np.array([[0]], dtype=np.float32))  # shape = [1,1]
        loc = tf.constant(np.array([[0, 0], [0, 0]], dtype=np.float32))  # shape = [2,2]
        with pytest.raises(ValueError) as err_info:
            layer_util.resample(vol=vol, loc=loc)
        assert "vol shape inconsistent with loc" in str(err_info.value)

    def test_interpolation_error(self):

        interpolation = "nearest"
        vol = tf.constant(np.array([[0]], dtype=np.float32))  # shape = [1,1]
        loc = tf.constant(np.array([[0, 0], [0, 0]], dtype=np.float32))  # shape = [2,2]
        with pytest.raises(ValueError) as err_info:
            layer_util.resample(vol=vol, loc=loc, interpolation=interpolation)
        assert "resample supports only linear interpolation" in str(err_info.value)


class TestWarpGrid:
    """
    Test warp_grid by confirming that it generates
    appropriate solutions for simple precomputed cases.
    """

    grid = tf.constant(
        np.array(
            [[[[0, 0, 0], [0, 0, 1], [0, 0, 2]], [[0, 1, 0], [0, 1, 1], [0, 1, 2]]]],
            dtype=np.float32,
        )
    )  # shape = (1, 2, 3, 3)

    def test_identical(self):

        theta = tf.constant(np.eye(4, 3).reshape((1, 4, 3)), dtype=tf.float32)
        expected = self.grid[None, ...]  # shape = (1, 1, 2, 3, 3)
        got = layer_util.warp_grid(grid=self.grid, theta=theta)
        assert is_equal_tf(got, expected)

    def test_non_identical(self):

        theta = tf.constant(
            np.array(
                [
                    [
                        [0.86, 0.75, 0.48],
                        [0.07, 0.98, 0.01],
                        [0.72, 0.52, 0.97],
                        [0.12, 0.4, 0.04],
                    ]
                ],
                dtype=np.float32,
            )
        )  # shape = (1, 4, 3)
        expected = tf.constant(
            np.array(
                [
                    [
                        [
                            [[0.12, 0.4, 0.04], [0.84, 0.92, 1.01], [1.56, 1.44, 1.98]],
                            [[0.19, 1.38, 0.05], [0.91, 1.9, 1.02], [1.63, 2.42, 1.99]],
                        ]
                    ]
                ],
                dtype=np.float32,
            )
        )  # shape = (1, 1, 2, 3, 3)
        got = layer_util.warp_grid(grid=self.grid, theta=theta)
        assert is_equal_tf(got, expected)


class TestGaussianFilter3D:

    @pytest.mark.parametrize(
        "kernel_sigma, kernel_size",
        [
            ((1, 1, 1), (3, 3, 3, 3, 3)),
            ((2, 2, 2), (7, 7, 7, 3, 3)),
            ((5, 5, 5), (15, 15, 15, 3, 3)),
            (1, (3, 3, 3, 3, 3)),
            (2, (7, 7, 7, 3, 3)),
            (5, (15, 15, 15, 3, 3)),
        ],

    )
    def test_kernel_size(self, kernel_sigma, kernel_size):
        filter = layer_util.gaussian_filter_3d(kernel_sigma)

        assert filter.shape == kernel_size

    @pytest.mark.parametrize(
        "kernel_sigma",
        [(1, 1, 1), (2, 2, 2), (5, 5, 5)],
    )

    def test_sum(self, kernel_sigma):
        filter = layer_util.gaussian_filter_3d(kernel_sigma)

        assert np.allclose(np.sum(filter), 3, atol=1e-3)


class TestDeconvOutputPadding:

    @pytest.mark.parametrize(
        ("input_shape", "output_shape", "kernel_size", "stride", "padding", "expected"),
        [
            (5, 5, 3, 1, "same", 0),
            (5, 7, 3, 1, "valid", 0),
            (5, 3, 3, 1, "full", 0),
            (5, 6, 3, 1, "same", 1),
            (5, 8, 3, 1, "valid", 1),
            (5, 4, 3, 1, "full", 1),
            (5, 9, 3, 2, "same", 0),
            (5, 11, 3, 2, "valid", 0),
            (5, 7, 3, 2, "full", 0),
        ],
    )
    def test_1d(
        self,
        input_shape: int,
        output_shape: int,
        kernel_size: int,
        stride: int,
        padding: str,
        expected: int,
    ):
        """
        Test _deconv_output_padding by verifying output

        :param input_shape: shape of Conv3DTranspose input tensor
        :param output_shape: shape of Conv3DTranspose output tensor
        :param kernel_size: kernel size of Conv3DTranspose layer
        :param stride: stride of Conv3DTranspose layer
        :param padding: padding of Conv3DTranspose layer
        :param expected: expected output padding for Conv3DTranspose layer
        """
        got = layer_util._deconv_output_padding(
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent
            input_shape, output_shape, kernel_size, stride, padding
        )
        assert got == expected

    def test_1d_err(self):
        """Test _deconv_output_padding err raising."""
        with pytest.raises(ValueError) as err_info:
            layer_util._deconv_output_padding(5, 5, 3, 1, "x")
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent
        assert "Unknown padding" in str(err_info.value)

    @pytest.mark.parametrize(
        ("input_shape", "output_shape", "kernel_size", "stride", "padding", "expected"),
        [
            (5, 9, 3, 2, "same", 0),
            ((5, 5), (9, 10), 3, 2, "same", (0, 1)),
            ((5, 5, 6), (9, 10, 12), 3, 2, "same", (0, 1, 1)),
            ((5, 5), (9, 10), (3, 3), 2, "same", (0, 1)),
            ((5, 5), (9, 10), 3, (2, 2), "same", (0, 1)),
            ((5, 5), (9, 10), (3, 4), 2, "same", (0, 2)),
        ],
    )
    def test_n_dim(
        self,
        input_shape: Union[Tuple[int, ...], int],
        output_shape: Union[Tuple[int, ...], int],
        kernel_size: Union[Tuple[int, ...], int],
        stride: Union[Tuple[int, ...], int],
        padding: str,
        expected: Union[Tuple[int, ...], int],
    ):
        """
        Test deconv_output_padding by verifying output

        :param input_shape: shape of Conv3DTranspose input tensor
        :param output_shape: shape of Conv3DTranspose output tensor
        :param kernel_size: kernel size of Conv3DTranspose layer
        :param stride: stride of Conv3DTranspose layer
        :param padding: padding of Conv3DTranspose layer
        :param expected: expected output padding for Conv3DTranspose layer
        """
        got = layer_util.deconv_output_padding(
            input_shape, output_shape, kernel_size, stride, padding
        )
        assert got == expected


1		"""
2		Tests for deepreg/model/layer_util.py in
3		pytest style
4		"""
5		from test.unit.util import is_equal_tf
6		from typing import Tuple, Union
7
8		import numpy as np
9		import pytest
10		import tensorflow as tf
11
12		import deepreg.model.layer_util as layer_util
13
14
15		def test_get_reference_grid():
16		"""
17		Test get_reference_grid by confirming that it generates
18		a sample grid test case to is_equal_tf's tolerance level.
19		"""
20		want = tf.constant(
21		np.array(
22		[[[[0, 0, 0], [0, 0, 1], [0, 0, 2]], [[0, 1, 0], [0, 1, 1], [0, 1, 2]]]],
23		dtype=np.float32,
24		)
25		)
26		get = layer_util.get_reference_grid(grid_size=[1, 2, 3])
27		assert is_equal_tf(want, get)
28
29
30		def test_get_n_bits_combinations():
31		"""
32		Test get_n_bits_combinations by confirming that it generates
33		appropriate solutions for 1D, 2D, and 3D cases.
34		"""
35		# Check n=1 - Pass
36		assert layer_util.get_n_bits_combinations(1) == [[0], [1]]
37		# Check n=2 - Pass
38		assert layer_util.get_n_bits_combinations(2) == [[0, 0], [0, 1], [1, 0], [1, 1]]
39
40		# Check n=3 - Pass
41		assert layer_util.get_n_bits_combinations(3) == [
42		[0, 0, 0],
43		[0, 0, 1],
44		[0, 1, 0],
45		[0, 1, 1],
46		[1, 0, 0],
47		[1, 0, 1],
48		[1, 1, 0],
49		[1, 1, 1],
50		]
51
52
53		class TestPyramidCombination:
		0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
54	View Code Duplication	def test_1d(self):
		0 ignored issues – show Duplication introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history... introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
55		weights = tf.constant(np.array([[0.2]], dtype=np.float32))
56		values = tf.constant(np.array([[1], [2]], dtype=np.float32))
57
58		# expected = 1 * 0.2 + 2 * 2
59		expected = tf.constant(np.array([1.8], dtype=np.float32))
60		got = layer_util.pyramid_combination(
61		values=values, weight_floor=weights, weight_ceil=1 - weights
62		)
63		assert is_equal_tf(got, expected)
64
65	View Code Duplication	def test_2d(self):
		0 ignored issues – show Duplication introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history... introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
66		weights = tf.constant(np.array([[0.2], [0.3]], dtype=np.float32))
67		values = tf.constant(
68		np.array(
69		[
70		[1], # value at corner (0, 0), weight = 0.2 * 0.3
71		[2], # value at corner (0, 1), weight = 0.2 * 0.7
72		[3], # value at corner (1, 0), weight = 0.8 * 0.3
73		[4], # value at corner (1, 1), weight = 0.8 * 0.7
74		],
75		dtype=np.float32,
76		)
77		)
78		# expected = 1 * 0.2 * 0.3
79		# + 2 * 0.2 * 0.7
80		# + 3 * 0.8 * 0.3
81		# + 4 * 0.8 * 0.7
82		expected = tf.constant(np.array([3.3], dtype=np.float32))
83		got = layer_util.pyramid_combination(
84		values=values, weight_floor=weights, weight_ceil=1 - weights
85		)
86		assert is_equal_tf(got, expected)
87
88		def test_error_dim(self):
		0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
89		weights = tf.constant(np.array([[[0.2]], [[0.2]]], dtype=np.float32))
90		values = tf.constant(np.array([[1], [2]], dtype=np.float32))
91		with pytest.raises(ValueError) as err_info:
92		layer_util.pyramid_combination(
93		values=values, weight_floor=weights, weight_ceil=1 - weights
94		)
95		assert (
96		"In pyramid_combination, elements of values, weight_floor, "
97		"and weight_ceil should have same dimension" in str(err_info.value)
98		)
99
100		def test_error_len(self):
		0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
101		weights = tf.constant(np.array([[0.2]], dtype=np.float32))
102		values = tf.constant(np.array([[1]], dtype=np.float32))
103		with pytest.raises(ValueError) as err_info:
104		layer_util.pyramid_combination(
105		values=values, weight_floor=weights, weight_ceil=1 - weights
106		)
107		assert (
108		"In pyramid_combination, num_dim = len(weight_floor), "
109		"len(values) must be 2 ** num_dim" in str(err_info.value)
110		)
111
112
113		class TestLinearResample:
		0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
114		x_min, x_max = 0, 2
115		y_min, y_max = 0, 2
116		# vol are values on grid [0,2]x[0,2]
117		# values on each point is 3x+y
118		# shape = (1,3,3)
119		vol = tf.constant(np.array([[[0, 1, 2], [3, 4, 5], [6, 7, 8]]]), dtype=tf.float32)
120		# loc are some points, especially
121		# shape = (1,4,3,2)
122		loc = tf.constant(
123		np.array(
124		[
125		[
126		[[0, 0], [0, 1], [1, 2]], # boundary corners
127		[[0.4, 0], [0.5, 2], [2, 1.7]], # boundary edge
128		[[-0.4, 0.7], [0, 3], [2, 3]], # outside boundary
129		[[0.4, 0.7], [1, 1], [0.6, 0.3]], # internal
130		]
131		]
132		),
133		dtype=tf.float32,
134		)
135
136		@pytest.mark.parametrize("channel", [0, 1, 2])
137		def test_repeat_extrapolation(self, channel):
		0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
138		x = self.loc[..., 0]
139		y = self.loc[..., 1]
140		x = tf.clip_by_value(x, self.x_min, self.x_max)
141		y = tf.clip_by_value(y, self.y_min, self.y_max)
142		expected = 3 * x + y
143
144		vol = self.vol
145		if channel > 0:
146		vol = tf.repeat(vol[..., None], channel, axis=-1)
147		expected = tf.repeat(expected[..., None], channel, axis=-1)
148
149		got = layer_util.resample(vol=vol, loc=self.loc, zero_boundary=False)
150		assert is_equal_tf(expected, got)
151
152		@pytest.mark.parametrize("channel", [0, 1, 2])
153		def test_repeat_zero_bound(self, channel):
		0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
154		x = self.loc[..., 0]
155		y = self.loc[..., 1]
156		expected = 3 * x + y
157		expected = (
158		expected
159		* tf.cast(x > self.x_min, tf.float32)
160		* tf.cast(x <= self.x_max, tf.float32)
161		)
162		expected = (
163		expected
164		* tf.cast(y > self.y_min, tf.float32)
165		* tf.cast(y <= self.y_max, tf.float32)
166		)
167
168		vol = self.vol
169		if channel > 0:
170		vol = tf.repeat(vol[..., None], channel, axis=-1)
171		expected = tf.repeat(expected[..., None], channel, axis=-1)
172
173		got = layer_util.resample(vol=vol, loc=self.loc, zero_boundary=True)
174		assert is_equal_tf(expected, got)
175
176		def test_shape_error(self):
		0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
177		vol = tf.constant(np.array([[0]], dtype=np.float32)) # shape = [1,1]
178		loc = tf.constant(np.array([[0, 0], [0, 0]], dtype=np.float32)) # shape = [2,2]
179		with pytest.raises(ValueError) as err_info:
180		layer_util.resample(vol=vol, loc=loc)
181		assert "vol shape inconsistent with loc" in str(err_info.value)
182
183		def test_interpolation_error(self):
		0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
184		interpolation = "nearest"
185		vol = tf.constant(np.array([[0]], dtype=np.float32)) # shape = [1,1]
186		loc = tf.constant(np.array([[0, 0], [0, 0]], dtype=np.float32)) # shape = [2,2]
187		with pytest.raises(ValueError) as err_info:
188		layer_util.resample(vol=vol, loc=loc, interpolation=interpolation)
189		assert "resample supports only linear interpolation" in str(err_info.value)
190
191
192		class TestWarpGrid:
193		"""
194		Test warp_grid by confirming that it generates
195		appropriate solutions for simple precomputed cases.
196		"""
197
198		grid = tf.constant(
199		np.array(
200		[[[[0, 0, 0], [0, 0, 1], [0, 0, 2]], [[0, 1, 0], [0, 1, 1], [0, 1, 2]]]],
201		dtype=np.float32,
202		)
203		) # shape = (1, 2, 3, 3)
204
205		def test_identical(self):
		0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
206		theta = tf.constant(np.eye(4, 3).reshape((1, 4, 3)), dtype=tf.float32)
207		expected = self.grid[None, ...] # shape = (1, 1, 2, 3, 3)
208		got = layer_util.warp_grid(grid=self.grid, theta=theta)
209		assert is_equal_tf(got, expected)
210
211		def test_non_identical(self):
		0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
212		theta = tf.constant(
213		np.array(
214		[
215		[
216		[0.86, 0.75, 0.48],
217		[0.07, 0.98, 0.01],
218		[0.72, 0.52, 0.97],
219		[0.12, 0.4, 0.04],
220		]
221		],
222		dtype=np.float32,
223		)
224		) # shape = (1, 4, 3)
225		expected = tf.constant(
226		np.array(
227		[
228		[
229		[
230		[[0.12, 0.4, 0.04], [0.84, 0.92, 1.01], [1.56, 1.44, 1.98]],
231		[[0.19, 1.38, 0.05], [0.91, 1.9, 1.02], [1.63, 2.42, 1.99]],
232		]
233		]
234		],
235		dtype=np.float32,
236		)
237		) # shape = (1, 1, 2, 3, 3)
238		got = layer_util.warp_grid(grid=self.grid, theta=theta)
239		assert is_equal_tf(got, expected)
240
241
242		class TestGaussianFilter3D:
		0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
243		@pytest.mark.parametrize(
244		"kernel_sigma, kernel_size",
245		[
246		((1, 1, 1), (3, 3, 3, 3, 3)),
247		((2, 2, 2), (7, 7, 7, 3, 3)),
248		((5, 5, 5), (15, 15, 15, 3, 3)),
249		(1, (3, 3, 3, 3, 3)),
250		(2, (7, 7, 7, 3, 3)),
251		(5, (15, 15, 15, 3, 3)),
252		],
		0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
253		)
254		def test_kernel_size(self, kernel_sigma, kernel_size):
255		filter = layer_util.gaussian_filter_3d(kernel_sigma)
		0 ignored issues – show Bug Best Practice introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report This seems to re-define the built-in `filter`. It is generally discouraged to redefine built-ins as this makes code very hard to read. Loading history...
256		assert filter.shape == kernel_size
257
258		@pytest.mark.parametrize(
259		"kernel_sigma",
260		[(1, 1, 1), (2, 2, 2), (5, 5, 5)],
261		)
		0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
262		def test_sum(self, kernel_sigma):
263		filter = layer_util.gaussian_filter_3d(kernel_sigma)
		0 ignored issues – show Bug Best Practice introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report This seems to re-define the built-in `filter`. It is generally discouraged to redefine built-ins as this makes code very hard to read. Loading history...
264		assert np.allclose(np.sum(filter), 3, atol=1e-3)
265
266
267		class TestDeconvOutputPadding:
		0 ignored issues – show introduced 2021-02-02 23:48 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
268		@pytest.mark.parametrize(
269		("input_shape", "output_shape", "kernel_size", "stride", "padding", "expected"),
270		[
271		(5, 5, 3, 1, "same", 0),
272		(5, 7, 3, 1, "valid", 0),
273		(5, 3, 3, 1, "full", 0),
274		(5, 6, 3, 1, "same", 1),
275		(5, 8, 3, 1, "valid", 1),
276		(5, 4, 3, 1, "full", 1),
277		(5, 9, 3, 2, "same", 0),
278		(5, 11, 3, 2, "valid", 0),
279		(5, 7, 3, 2, "full", 0),
280		],
281		)
282		def test_1d(
283		self,
284		input_shape: int,
285		output_shape: int,
286		kernel_size: int,
287		stride: int,
288		padding: str,
289		expected: int,
290		):
291		"""
292		Test _deconv_output_padding by verifying output
293
294		:param input_shape: shape of Conv3DTranspose input tensor
295		:param output_shape: shape of Conv3DTranspose output tensor
296		:param kernel_size: kernel size of Conv3DTranspose layer
297		:param stride: stride of Conv3DTranspose layer
298		:param padding: padding of Conv3DTranspose layer
299		:param expected: expected output padding for Conv3DTranspose layer
300		"""
301		got = layer_util._deconv_output_padding(
		0 ignored issues – show Coding Style Best Practice introduced 2021-02-02 23:29 UTC by Report Bug Copy Issue Report It seems like `_deconv_output_padding` was declared protected and should not be accessed from this context. Prefixing a member variable `_` is usually regarded as the equivalent of declaring it with protected visibility that exists in other languages. Consequentially, such a member should only be accessed from the same class or a child class: class MyParent: def __init__(self): self._x = 1; self.y = 2; class MyChild(MyParent): def some_method(self): return self._x # Ok, since accessed from a child class class AnotherClass: def some_method(self, instance_of_my_child): return instance_of_my_child._x # Would be flagged as AnotherClass is not # a child class of MyParent Loading history...
302		input_shape, output_shape, kernel_size, stride, padding
303		)
304		assert got == expected
305
306		def test_1d_err(self):
307		"""Test _deconv_output_padding err raising."""
308		with pytest.raises(ValueError) as err_info:
309		layer_util._deconv_output_padding(5, 5, 3, 1, "x")
		0 ignored issues – show Coding Style Best Practice introduced 2021-02-02 23:48 UTC by Report Bug Copy Issue Report It seems like `_deconv_output_padding` was declared protected and should not be accessed from this context. Prefixing a member variable `_` is usually regarded as the equivalent of declaring it with protected visibility that exists in other languages. Consequentially, such a member should only be accessed from the same class or a child class: class MyParent: def __init__(self): self._x = 1; self.y = 2; class MyChild(MyParent): def some_method(self): return self._x # Ok, since accessed from a child class class AnotherClass: def some_method(self, instance_of_my_child): return instance_of_my_child._x # Would be flagged as AnotherClass is not # a child class of MyParent Loading history...
310		assert "Unknown padding" in str(err_info.value)
311
312		@pytest.mark.parametrize(
313		("input_shape", "output_shape", "kernel_size", "stride", "padding", "expected"),
314		[
315		(5, 9, 3, 2, "same", 0),
316		((5, 5), (9, 10), 3, 2, "same", (0, 1)),
317		((5, 5, 6), (9, 10, 12), 3, 2, "same", (0, 1, 1)),
318		((5, 5), (9, 10), (3, 3), 2, "same", (0, 1)),
319		((5, 5), (9, 10), 3, (2, 2), "same", (0, 1)),
320		((5, 5), (9, 10), (3, 4), 2, "same", (0, 2)),
321		],
322		)
323		def test_n_dim(
324		self,
325		input_shape: Union[Tuple[int, ...], int],
326		output_shape: Union[Tuple[int, ...], int],
327		kernel_size: Union[Tuple[int, ...], int],
328		stride: Union[Tuple[int, ...], int],
329		padding: str,
330		expected: Union[Tuple[int, ...], int],
331		):
332		"""
333		Test deconv_output_padding by verifying output
334
335		:param input_shape: shape of Conv3DTranspose input tensor
336		:param output_shape: shape of Conv3DTranspose output tensor
337		:param kernel_size: kernel size of Conv3DTranspose layer
338		:param stride: stride of Conv3DTranspose layer
339		:param padding: padding of Conv3DTranspose layer
340		:param expected: expected output padding for Conv3DTranspose layer
341		"""
342		got = layer_util.deconv_output_padding(
343		input_shape, output_shape, kernel_size, stride, padding
344		)
345		assert got == expected
346

DeepRegNet / DeepReg

Pull Request — main (#675)

test.unit.test_layer_util A

Complexity

Size/Duplication

Importance

15 Methods

2 Functions

How to fix Duplicated Code

Duplicated Code

Duplication Side-by-Side

Filter issues like