test.unit.test_nifti_loader.TestNiftiFileLoader.test_init() - Code Metrics - DeepRegNet/DeepReg - Measure and Improve Code Quality continuously with Scrutinizer

TestNiftiFileLoader.test_init() B
last analyzed 2022-05-18 21:56 UTC

↳ Parent: test.unit.test_nifti_loader

Complexity

Conditions

Size

Total Lines	115
Code Lines	89

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	89
dl	0
loc	115
rs	7.36
c	0
b	0
f	0
cc	1
nop	3

How to fix Long Method

"""
Tests functionality of the NiftiFileLoader
"""
import os
from test.unit.util import is_equal_np

import numpy as np
import pytest

from deepreg.dataset.loader.nifti_loader import NiftiFileLoader, load_nifti_file


def get_loader(loader_name):
    if loader_name in [

        "paired",
        "unpaired",
        "grouped",
    ]:
        dir_paths = [f"./data/test/nifti/{loader_name}/test"]
        name = "fixed_images" if loader_name == "paired" else "images"
        grouped = loader_name == "grouped"
    elif loader_name == "multi_dirs_grouped":
        dir_paths = [
            "./data/test/nifti/grouped/train",
            "./data/test/nifti/grouped/test",
        ]
        name = "images"
        grouped = True
    else:
        raise ValueError
    loader = NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=grouped)
    return loader


@pytest.mark.parametrize(
    "path,shape",
    [
        ("./data/test/nifti/paired/test/fixed_images/case000026.nii.gz", (44, 59, 41)),
        ("./data/test/nifti/unit_test/case000026.nii", (44, 59, 41)),
    ],
)
def test_load_nifti_file(path, shape):
    arr = load_nifti_file(file_path=path)
    assert arr.shape == shape


def test_load_nifti_file_err():
    h5_filepath = "./data/test/h5/paired/test/fixed_images.h5"
    with pytest.raises(ValueError) as err_info:
        load_nifti_file(file_path=h5_filepath)
    assert "Nifti file path must end with .nii or .nii.gz" in str(err_info.value)


class TestNiftiFileLoader:
    @pytest.mark.parametrize(
        "name,expected",
        [
            (
                "paired",
                [
                    [
                        ("./data/test/nifti/paired/test", "case000025", "nii.gz"),
                        ("./data/test/nifti/paired/test", "case000026", "nii.gz"),
                    ],
                    None,
                ],
            ),
            (
                "unpaired",
                [
                    [
                        ("./data/test/nifti/unpaired/test", "case000025", "nii.gz"),
                        ("./data/test/nifti/unpaired/test", "case000026", "nii"),
                    ],
                    None,
                ],
            ),
            (
                "grouped",
                [
                    [
                        (
                            "./data/test/nifti/grouped/test",
                            "group1",
                            "case000025",
                            "nii.gz",
                        ),
                        (
                            "./data/test/nifti/grouped/test",
                            "group1",
                            "case000026",
                            "nii.gz",
                        ),
                    ],
                    [[0, 1]],
                ],
            ),
            (
                "multi_dirs_grouped",
                [
                    [
                        (
                            "./data/test/nifti/grouped/test",
                            "group1",
                            "case000025",
                            "nii.gz",
                        ),
                        (
                            "./data/test/nifti/grouped/test",
                            "group1",
                            "case000026",
                            "nii.gz",
                        ),
                        (
                            "./data/test/nifti/grouped/train",
                            "group1",
                            "case000000",
                            "nii.gz",
                        ),
                        (
                            "./data/test/nifti/grouped/train",
                            "group1",
                            "case000001",
                            "nii.gz",
                        ),
                        (
                            "./data/test/nifti/grouped/train",
                            "group1",
                            "case000003",
                            "nii.gz",
                        ),
                        (
                            "./data/test/nifti/grouped/train",
                            "group1",
                            "case000008",
                            "nii.gz",
                        ),
                        (
                            "./data/test/nifti/grouped/train",
                            "group2",
                            "case000009",
                            "nii.gz",
                        ),
                        (
                            "./data/test/nifti/grouped/train",
                            "group2",
                            "case000011",
                            "nii.gz",
                        ),
                        (
                            "./data/test/nifti/grouped/train",
                            "group2",
                            "case000012",
                            "nii.gz",
                        ),
                    ],
                    [[0, 1], [2, 3, 4, 5], [6, 7, 8]],
                ],
            ),
        ],
    )
    def test_init(self, name, expected):
        loader = get_loader(name)
        got = [
            loader.data_path_splits,
            loader.group_struct,
        ]
        assert got == expected
        loader.close()

    @pytest.mark.parametrize(
        "name",
        [
            "paired",
            "unpaired",
            "grouped",
        ],
    )
    def test_init_duplicated_dirs(self, name):
        # duplicated dir_paths
        loader = get_loader(name)
        dir_paths = loader.dir_paths * 2
        with pytest.raises(ValueError) as err_info:
            NiftiFileLoader(
                dir_paths=dir_paths, name=loader.name, grouped=loader.grouped
            )
        assert "dir_paths have repeated elements" in str(err_info.value)
        loader.close()

    @pytest.mark.parametrize(
        "name,err_msg",
        [
            (
                "images",
                "directory ./data/test/h5/paired/test/images does not exist",
            ),  # test not existed files
        ],
    )
    def test_set_data_structure_err1(self, name, err_msg):
        dir_paths = ["./data/test/h5/paired/test"]
        with pytest.raises(AssertionError) as err_info:
            NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=True)
        assert err_msg in str(err_info.value)

    def test_set_data_structure_err2(self):
        dir_paths = ["./data/test/nifti/paired/test"]
        name = "error"
        dir_path = os.path.join(dir_paths[0], name)
        os.makedirs(dir_path, exist_ok=True)
        with pytest.raises(ValueError) as err_info:
            NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=False)
        assert "No data collected" in str(err_info.value)
        os.removedirs(dir_path)

    @pytest.mark.parametrize(

        "name,index,expected",
        [
            ("paired", 0, [(44, 59, 41), [255.0, 0.0, 68.359276, 65.84009]]),
            ("unpaired", 0, [(64, 64, 60), [255.0, 0.0, 60.073948, 47.27648]]),
            ("grouped", (0, 1), [(64, 64, 60), [255.0, 0.0, 85.67942, 49.193127]]),
            (
                "multi_dirs_grouped",
                (0, 1),
                [(64, 64, 60), [255.0, 0.0, 85.67942, 49.193127]],
            ),
        ],
    )
    def test_get_data(self, name, index, expected):
        loader = get_loader(name)
        array = loader.get_data(index)
        got = [
            np.shape(array),
            [np.amax(array), np.amin(array), np.mean(array), np.std(array)],
        ]
        assert got[0] == expected[0]
        assert is_equal_np(got[1], expected[1])
        loader.close()

    @pytest.mark.parametrize(

        "name,expected",
        [
            (
                "paired",
                [
                    ("./data/test/nifti/paired/test", "case000025"),
                    ("./data/test/nifti/paired/test", "case000026"),
                ],
            ),
            (
                "unpaired",
                [
                    ("./data/test/nifti/unpaired/test", "case000025"),
                    ("./data/test/nifti/unpaired/test", "case000026"),
                ],
            ),
            (
                "grouped",
                [
                    ("./data/test/nifti/grouped/test", "group1", "case000025"),
                    ("./data/test/nifti/grouped/test", "group1", "case000026"),
                ],
            ),
            (
                "multi_dirs_grouped",
                [
                    ("./data/test/nifti/grouped/test", "group1", "case000025"),
                    ("./data/test/nifti/grouped/test", "group1", "case000026"),
                    ("./data/test/nifti/grouped/train", "group1", "case000000"),
                    ("./data/test/nifti/grouped/train", "group1", "case000001"),
                    ("./data/test/nifti/grouped/train", "group1", "case000003"),
                    ("./data/test/nifti/grouped/train", "group1", "case000008"),
                    ("./data/test/nifti/grouped/train", "group2", "case000009"),
                    ("./data/test/nifti/grouped/train", "group2", "case000011"),
                    ("./data/test/nifti/grouped/train", "group2", "case000012"),
                ],
            ),
        ],
    )
    def test_get_data_ids(self, name, expected):
        loader = get_loader(name)
        got = loader.get_data_ids()
        assert got == expected
        loader.close()

    @pytest.mark.parametrize(
        "index,err_type",
        [
            (-1, AssertionError),
            (64, IndexError),
            ((0, 1), AssertionError),
            ("wrong", ValueError),
        ],
    )
    def test_get_data_ids_check_err_with_paired(self, index, err_type):
        # wrong index for paired
        loader = get_loader("paired")
        with pytest.raises(err_type):
            loader.get_data(index=index)
        loader.close()

    def test_get_data_ids_check_err_with_grouped(self):
        # wrong index for paired
        loader = get_loader("grouped")
        with pytest.raises(AssertionError):
            # non-tuple data_index
            loader.get_data(index=1)
        loader.close()

    @pytest.mark.parametrize(
        "name,expected",
        [("paired", 2), ("unpaired", 2), ("grouped", 2), ("multi_dirs_grouped", 9)],
    )
    def test_get_num_images(self, name, expected):
        loader = get_loader(name)
        got = loader.get_num_images()
        assert got == expected
        loader.close()

    @pytest.mark.parametrize(
        "name",
        [
            "paired",
            "unpaired",
            "grouped",
        ],
    )
    def test_close(self, name):
        loader = get_loader(name)
        loader.close()


1		"""
2		Tests functionality of the NiftiFileLoader
3		"""
4		import os
5		from test.unit.util import is_equal_np
6
7		import numpy as np
8		import pytest
9
10		from deepreg.dataset.loader.nifti_loader import NiftiFileLoader, load_nifti_file
11
12
13		def get_loader(loader_name):
14	View Code Duplication	if loader_name in [
		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...
15		"paired",
16		"unpaired",
17		"grouped",
18		]:
19		dir_paths = [f"./data/test/nifti/{loader_name}/test"]
20		name = "fixed_images" if loader_name == "paired" else "images"
21		grouped = loader_name == "grouped"
22		elif loader_name == "multi_dirs_grouped":
23		dir_paths = [
24		"./data/test/nifti/grouped/train",
25		"./data/test/nifti/grouped/test",
26		]
27		name = "images"
28		grouped = True
29		else:
30		raise ValueError
31		loader = NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=grouped)
32		return loader
33
34
35		@pytest.mark.parametrize(
36		"path,shape",
37		[
38		("./data/test/nifti/paired/test/fixed_images/case000026.nii.gz", (44, 59, 41)),
39		("./data/test/nifti/unit_test/case000026.nii", (44, 59, 41)),
40		],
41		)
42		def test_load_nifti_file(path, shape):
43		arr = load_nifti_file(file_path=path)
44		assert arr.shape == shape
45
46
47		def test_load_nifti_file_err():
48		h5_filepath = "./data/test/h5/paired/test/fixed_images.h5"
49		with pytest.raises(ValueError) as err_info:
50		load_nifti_file(file_path=h5_filepath)
51		assert "Nifti file path must end with .nii or .nii.gz" in str(err_info.value)
52
53
54		class TestNiftiFileLoader:
55		@pytest.mark.parametrize(
56		"name,expected",
57		[
58		(
59		"paired",
60		[
61		[
62		("./data/test/nifti/paired/test", "case000025", "nii.gz"),
63		("./data/test/nifti/paired/test", "case000026", "nii.gz"),
64		],
65		None,
66		],
67		),
68		(
69		"unpaired",
70		[
71		[
72		("./data/test/nifti/unpaired/test", "case000025", "nii.gz"),
73		("./data/test/nifti/unpaired/test", "case000026", "nii"),
74		],
75		None,
76		],
77		),
78		(
79		"grouped",
80		[
81		[
82		(
83		"./data/test/nifti/grouped/test",
84		"group1",
85		"case000025",
86		"nii.gz",
87		),
88		(
89		"./data/test/nifti/grouped/test",
90		"group1",
91		"case000026",
92		"nii.gz",
93		),
94		],
95		[[0, 1]],
96		],
97		),
98		(
99		"multi_dirs_grouped",
100		[
101		[
102		(
103		"./data/test/nifti/grouped/test",
104		"group1",
105		"case000025",
106		"nii.gz",
107		),
108		(
109		"./data/test/nifti/grouped/test",
110		"group1",
111		"case000026",
112		"nii.gz",
113		),
114		(
115		"./data/test/nifti/grouped/train",
116		"group1",
117		"case000000",
118		"nii.gz",
119		),
120		(
121		"./data/test/nifti/grouped/train",
122		"group1",
123		"case000001",
124		"nii.gz",
125		),
126		(
127		"./data/test/nifti/grouped/train",
128		"group1",
129		"case000003",
130		"nii.gz",
131		),
132		(
133		"./data/test/nifti/grouped/train",
134		"group1",
135		"case000008",
136		"nii.gz",
137		),
138		(
139		"./data/test/nifti/grouped/train",
140		"group2",
141		"case000009",
142		"nii.gz",
143		),
144		(
145		"./data/test/nifti/grouped/train",
146		"group2",
147		"case000011",
148		"nii.gz",
149		),
150		(
151		"./data/test/nifti/grouped/train",
152		"group2",
153		"case000012",
154		"nii.gz",
155		),
156		],
157		[[0, 1], [2, 3, 4, 5], [6, 7, 8]],
158		],
159		),
160		],
161		)
162		def test_init(self, name, expected):
163		loader = get_loader(name)
164		got = [
165		loader.data_path_splits,
166		loader.group_struct,
167		]
168		assert got == expected
169		loader.close()
170
171		@pytest.mark.parametrize(
172		"name",
173		[
174		"paired",
175		"unpaired",
176		"grouped",
177		],
178		)
179		def test_init_duplicated_dirs(self, name):
180		# duplicated dir_paths
181		loader = get_loader(name)
182		dir_paths = loader.dir_paths * 2
183		with pytest.raises(ValueError) as err_info:
184		NiftiFileLoader(
185		dir_paths=dir_paths, name=loader.name, grouped=loader.grouped
186		)
187		assert "dir_paths have repeated elements" in str(err_info.value)
188		loader.close()
189
190		@pytest.mark.parametrize(
191		"name,err_msg",
192		[
193		(
194		"images",
195		"directory ./data/test/h5/paired/test/images does not exist",
196		), # test not existed files
197		],
198		)
199		def test_set_data_structure_err1(self, name, err_msg):
200		dir_paths = ["./data/test/h5/paired/test"]
201		with pytest.raises(AssertionError) as err_info:
202		NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=True)
203		assert err_msg in str(err_info.value)
204
205		def test_set_data_structure_err2(self):
206		dir_paths = ["./data/test/nifti/paired/test"]
207		name = "error"
208		dir_path = os.path.join(dir_paths[0], name)
209		os.makedirs(dir_path, exist_ok=True)
210		with pytest.raises(ValueError) as err_info:
211		NiftiFileLoader(dir_paths=dir_paths, name=name, grouped=False)
212		assert "No data collected" in str(err_info.value)
213		os.removedirs(dir_path)
214
215	View Code Duplication	@pytest.mark.parametrize(
		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...
216		"name,index,expected",
217		[
218		("paired", 0, [(44, 59, 41), [255.0, 0.0, 68.359276, 65.84009]]),
219		("unpaired", 0, [(64, 64, 60), [255.0, 0.0, 60.073948, 47.27648]]),
220		("grouped", (0, 1), [(64, 64, 60), [255.0, 0.0, 85.67942, 49.193127]]),
221		(
222		"multi_dirs_grouped",
223		(0, 1),
224		[(64, 64, 60), [255.0, 0.0, 85.67942, 49.193127]],
225		),
226		],
227		)
228		def test_get_data(self, name, index, expected):
229		loader = get_loader(name)
230		array = loader.get_data(index)
231		got = [
232		np.shape(array),
233		[np.amax(array), np.amin(array), np.mean(array), np.std(array)],
234		]
235		assert got[0] == expected[0]
236		assert is_equal_np(got[1], expected[1])
237		loader.close()
238
239	View Code Duplication	@pytest.mark.parametrize(
		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...
240		"name,expected",
241		[
242		(
243		"paired",
244		[
245		("./data/test/nifti/paired/test", "case000025"),
246		("./data/test/nifti/paired/test", "case000026"),
247		],
248		),
249		(
250		"unpaired",
251		[
252		("./data/test/nifti/unpaired/test", "case000025"),
253		("./data/test/nifti/unpaired/test", "case000026"),
254		],
255		),
256		(
257		"grouped",
258		[
259		("./data/test/nifti/grouped/test", "group1", "case000025"),
260		("./data/test/nifti/grouped/test", "group1", "case000026"),
261		],
262		),
263		(
264		"multi_dirs_grouped",
265		[
266		("./data/test/nifti/grouped/test", "group1", "case000025"),
267		("./data/test/nifti/grouped/test", "group1", "case000026"),
268		("./data/test/nifti/grouped/train", "group1", "case000000"),
269		("./data/test/nifti/grouped/train", "group1", "case000001"),
270		("./data/test/nifti/grouped/train", "group1", "case000003"),
271		("./data/test/nifti/grouped/train", "group1", "case000008"),
272		("./data/test/nifti/grouped/train", "group2", "case000009"),
273		("./data/test/nifti/grouped/train", "group2", "case000011"),
274		("./data/test/nifti/grouped/train", "group2", "case000012"),
275		],
276		),
277		],
278		)
279		def test_get_data_ids(self, name, expected):
280		loader = get_loader(name)
281		got = loader.get_data_ids()
282		assert got == expected
283		loader.close()
284
285		@pytest.mark.parametrize(
286		"index,err_type",
287		[
288		(-1, AssertionError),
289		(64, IndexError),
290		((0, 1), AssertionError),
291		("wrong", ValueError),
292		],
293		)
294		def test_get_data_ids_check_err_with_paired(self, index, err_type):
295		# wrong index for paired
296		loader = get_loader("paired")
297		with pytest.raises(err_type):
298		loader.get_data(index=index)
299		loader.close()
300
301		def test_get_data_ids_check_err_with_grouped(self):
302		# wrong index for paired
303		loader = get_loader("grouped")
304		with pytest.raises(AssertionError):
305		# non-tuple data_index
306		loader.get_data(index=1)
307		loader.close()
308
309		@pytest.mark.parametrize(
310		"name,expected",
311		[("paired", 2), ("unpaired", 2), ("grouped", 2), ("multi_dirs_grouped", 9)],
312		)
313		def test_get_num_images(self, name, expected):
314		loader = get_loader(name)
315		got = loader.get_num_images()
316		assert got == expected
317		loader.close()
318
319		@pytest.mark.parametrize(
320		"name",
321		[
322		"paired",
323		"unpaired",
324		"grouped",
325		],
326		)
327		def test_close(self, name):
328		loader = get_loader(name)
329		loader.close()
330

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TestNiftiFileLoader.test_init() B last analyzed 2022-05-18 21:56 UTC

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TestNiftiFileLoader.test_init() B
last analyzed 2022-05-18 21:56 UTC