test.unit.test_layer_util.test_resize3d() - 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 2021-01-30 23:52 UTC

test.unit.test_layer_util.test_resize3d() B

↳ Parent: Project

Complexity

Conditions

Size

Total Lines	75
Code Lines	52

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	52
dl	0
loc	75
rs	8.5709
c	0
b	0
f	0
cc	3
nop	0

How to fix Long Method

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

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)


1		"""
2		Tests for deepreg/model/layer_util.py in
3		pytest style
4		"""
5		from test.unit.util import is_equal_tf
6
7		import numpy as np
8		import pytest
9		import tensorflow as tf
10
11		import deepreg.model.layer_util as layer_util
12
13
14		def test_get_reference_grid():
15		"""
16		Test get_reference_grid by confirming that it generates
17		a sample grid test case to is_equal_tf's tolerance level.
18		"""
19		want = tf.constant(
20		np.array(
21		[[[[0, 0, 0], [0, 0, 1], [0, 0, 2]], [[0, 1, 0], [0, 1, 1], [0, 1, 2]]]],
22		dtype=np.float32,
23		)
24		)
25		get = layer_util.get_reference_grid(grid_size=[1, 2, 3])
26		assert is_equal_tf(want, get)
27
28
29		def test_get_n_bits_combinations():
30		"""
31		Test get_n_bits_combinations by confirming that it generates
32		appropriate solutions for 1D, 2D, and 3D cases.
33		"""
34		# Check n=1 - Pass
35		assert layer_util.get_n_bits_combinations(1) == [[0], [1]]
36		# Check n=2 - Pass
37		assert layer_util.get_n_bits_combinations(2) == [[0, 0], [0, 1], [1, 0], [1, 1]]
38
39		# Check n=3 - Pass
40		assert layer_util.get_n_bits_combinations(3) == [
41		[0, 0, 0],
42		[0, 0, 1],
43		[0, 1, 0],
44		[0, 1, 1],
45		[1, 0, 0],
46		[1, 0, 1],
47		[1, 1, 0],
48		[1, 1, 1],
49		]
50
51
52		class TestPyramidCombination:
		0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
53	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...
54		weights = tf.constant(np.array([[0.2]], dtype=np.float32))
55		values = tf.constant(np.array([[1], [2]], dtype=np.float32))
56
57		# expected = 1 * 0.2 + 2 * 2
58		expected = tf.constant(np.array([1.8], dtype=np.float32))
59		got = layer_util.pyramid_combination(
60		values=values, weight_floor=weights, weight_ceil=1 - weights
61		)
62		assert is_equal_tf(got, expected)
63
64	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...
65		weights = tf.constant(np.array([[0.2], [0.3]], dtype=np.float32))
66		values = tf.constant(
67		np.array(
68		[
69		[1], # value at corner (0, 0), weight = 0.2 * 0.3
70		[2], # value at corner (0, 1), weight = 0.2 * 0.7
71		[3], # value at corner (1, 0), weight = 0.8 * 0.3
72		[4], # value at corner (1, 1), weight = 0.8 * 0.7
73		],
74		dtype=np.float32,
75		)
76		)
77		# expected = 1 * 0.2 * 0.3
78		# + 2 * 0.2 * 0.7
79		# + 3 * 0.8 * 0.3
80		# + 4 * 0.8 * 0.7
81		expected = tf.constant(np.array([3.3], dtype=np.float32))
82		got = layer_util.pyramid_combination(
83		values=values, weight_floor=weights, weight_ceil=1 - weights
84		)
85		assert is_equal_tf(got, expected)
86
87		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...
88		weights = tf.constant(np.array([[[0.2]], [[0.2]]], dtype=np.float32))
89		values = tf.constant(np.array([[1], [2]], dtype=np.float32))
90		with pytest.raises(ValueError) as err_info:
91		layer_util.pyramid_combination(
92		values=values, weight_floor=weights, weight_ceil=1 - weights
93		)
94		assert (
95		"In pyramid_combination, elements of values, weight_floor, "
96		"and weight_ceil should have same dimension" in str(err_info.value)
97		)
98
99		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...
100		weights = tf.constant(np.array([[0.2]], dtype=np.float32))
101		values = tf.constant(np.array([[1]], dtype=np.float32))
102		with pytest.raises(ValueError) as err_info:
103		layer_util.pyramid_combination(
104		values=values, weight_floor=weights, weight_ceil=1 - weights
105		)
106		assert (
107		"In pyramid_combination, num_dim = len(weight_floor), "
108		"len(values) must be 2 ** num_dim" in str(err_info.value)
109		)
110
111
112		class TestLinearResample:
		0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
113		x_min, x_max = 0, 2
114		y_min, y_max = 0, 2
115		# vol are values on grid [0,2]x[0,2]
116		# values on each point is 3x+y
117		# shape = (1,3,3)
118		vol = tf.constant(np.array([[[0, 1, 2], [3, 4, 5], [6, 7, 8]]]), dtype=tf.float32)
119		# loc are some points, especially
120		# shape = (1,4,3,2)
121		loc = tf.constant(
122		np.array(
123		[
124		[
125		[[0, 0], [0, 1], [1, 2]], # boundary corners
126		[[0.4, 0], [0.5, 2], [2, 1.7]], # boundary edge
127		[[-0.4, 0.7], [0, 3], [2, 3]], # outside boundary
128		[[0.4, 0.7], [1, 1], [0.6, 0.3]], # internal
129		]
130		]
131		),
132		dtype=tf.float32,
133		)
134
135		@pytest.mark.parametrize("channel", [0, 1, 2])
136		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...
137		x = self.loc[..., 0]
138		y = self.loc[..., 1]
139		x = tf.clip_by_value(x, self.x_min, self.x_max)
140		y = tf.clip_by_value(y, self.y_min, self.y_max)
141		expected = 3 * x + y
142
143		vol = self.vol
144		if channel > 0:
145		vol = tf.repeat(vol[..., None], channel, axis=-1)
146		expected = tf.repeat(expected[..., None], channel, axis=-1)
147
148		got = layer_util.resample(vol=vol, loc=self.loc, zero_boundary=False)
149		assert is_equal_tf(expected, got)
150
151		@pytest.mark.parametrize("channel", [0, 1, 2])
152		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...
153		x = self.loc[..., 0]
154		y = self.loc[..., 1]
155		expected = 3 * x + y
156		expected = (
157		expected
158		* tf.cast(x > self.x_min, tf.float32)
159		* tf.cast(x <= self.x_max, tf.float32)
160		)
161		expected = (
162		expected
163		* tf.cast(y > self.y_min, tf.float32)
164		* tf.cast(y <= self.y_max, tf.float32)
165		)
166
167		vol = self.vol
168		if channel > 0:
169		vol = tf.repeat(vol[..., None], channel, axis=-1)
170		expected = tf.repeat(expected[..., None], channel, axis=-1)
171
172		got = layer_util.resample(vol=vol, loc=self.loc, zero_boundary=True)
173		assert is_equal_tf(expected, got)
174
175		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...
176		vol = tf.constant(np.array([[0]], dtype=np.float32)) # shape = [1,1]
177		loc = tf.constant(np.array([[0, 0], [0, 0]], dtype=np.float32)) # shape = [2,2]
178		with pytest.raises(ValueError) as err_info:
179		layer_util.resample(vol=vol, loc=loc)
180		assert "vol shape inconsistent with loc" in str(err_info.value)
181
182		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...
183		interpolation = "nearest"
184		vol = tf.constant(np.array([[0]], dtype=np.float32)) # shape = [1,1]
185		loc = tf.constant(np.array([[0, 0], [0, 0]], dtype=np.float32)) # shape = [2,2]
186		with pytest.raises(ValueError) as err_info:
187		layer_util.resample(vol=vol, loc=loc, interpolation=interpolation)
188		assert "resample supports only linear interpolation" in str(err_info.value)
189
190
191		class TestWarpGrid:
192		"""
193		Test warp_grid by confirming that it generates
194		appropriate solutions for simple precomputed cases.
195		"""
196
197		grid = tf.constant(
198		np.array(
199		[[[[0, 0, 0], [0, 0, 1], [0, 0, 2]], [[0, 1, 0], [0, 1, 1], [0, 1, 2]]]],
200		dtype=np.float32,
201		)
202		) # shape = (1, 2, 3, 3)
203
204		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...
205		theta = tf.constant(np.eye(4, 3).reshape((1, 4, 3)), dtype=tf.float32)
206		expected = self.grid[None, ...] # shape = (1, 1, 2, 3, 3)
207		got = layer_util.warp_grid(grid=self.grid, theta=theta)
208		assert is_equal_tf(got, expected)
209
210		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...
211		theta = tf.constant(
212		np.array(
213		[
214		[
215		[0.86, 0.75, 0.48],
216		[0.07, 0.98, 0.01],
217		[0.72, 0.52, 0.97],
218		[0.12, 0.4, 0.04],
219		]
220		],
221		dtype=np.float32,
222		)
223		) # shape = (1, 4, 3)
224		expected = tf.constant(
225		np.array(
226		[
227		[
228		[
229		[[0.12, 0.4, 0.04], [0.84, 0.92, 1.01], [1.56, 1.44, 1.98]],
230		[[0.19, 1.38, 0.05], [0.91, 1.9, 1.02], [1.63, 2.42, 1.99]],
231		]
232		]
233		],
234		dtype=np.float32,
235		)
236		) # shape = (1, 1, 2, 3, 3)
237		got = layer_util.warp_grid(grid=self.grid, theta=theta)
238		assert is_equal_tf(got, expected)
239
240
241		class TestGaussianFilter3D:
		0 ignored issues – show introduced 2021-01-30 23:31 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
242		@pytest.mark.parametrize(
243		"kernel_sigma, kernel_size",
244		[
245		((1, 1, 1), (3, 3, 3, 3, 3)),
246		((2, 2, 2), (7, 7, 7, 3, 3)),
247		((5, 5, 5), (15, 15, 15, 3, 3)),
248		(1, (3, 3, 3, 3, 3)),
249		(2, (7, 7, 7, 3, 3)),
250		(5, (15, 15, 15, 3, 3)),
251		],
		0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
252		)
253		def test_kernel_size(self, kernel_sigma, kernel_size):
254		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...
255		assert filter.shape == kernel_size
256
257		@pytest.mark.parametrize(
258		"kernel_sigma",
259		[(1, 1, 1), (2, 2, 2), (5, 5, 5)],
260		)
		0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
261		def test_sum(self, kernel_sigma):
262		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...
263		assert np.allclose(np.sum(filter), 3, atol=1e-3)
264

DeepRegNet / DeepReg

Pull Request — main (#656)

test.unit.test_layer_util.test_resize3d() B

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