test.unit.test_config_parser.test_config_sanity_check() - Code Metrics - Inspection of "647 refactor optimizer config" - DeepRegNet/DeepReg - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Pull Request — main (#651)

by Yunguan

created 2021-01-26 10:14 UTC

test_config_sanity_check() C

↳ Parent: test.unit.test_config_parser

Complexity

Conditions

Size

Total Lines	97
Code Lines	60

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	60
dl	0
loc	97
rs	6.909
c	0
b	0
f	0
cc	7
nop	1

How to fix Long Method

"""
Tests functions in config/parser.py
"""

import os

import pytest
import yaml
from testfixtures import TempDirectory

from deepreg.config.parser import (
    config_sanity_check,
    load_configs,
    save,
    update_nested_dict,
)


def test_update_nested_dict():
    """test update_nested_dict by checking outputs values"""
    # two simple dicts with different keys
    d = dict(d=1)
    v = dict(v=0)
    got = update_nested_dict(d, v)
    expected = dict(d=1, v=0)
    assert got == expected

    # two simple dicts with same key
    d = dict(d=1)
    v = dict(d=0)
    got = update_nested_dict(d, v)
    expected = dict(d=0)
    assert got == expected

    # dict with nested dict without common key
    d = dict(d=1)
    v = dict(v=dict(x=0))
    got = update_nested_dict(d, v)
    expected = dict(d=1, v=dict(x=0))
    assert got == expected

    # dict with nested dict with common key
    # fail because can not use dict to overwrite non dict values
    d = dict(v=1)
    v = dict(v=dict(x=0))
    with pytest.raises(TypeError) as err_info:
        update_nested_dict(d, v)
    assert "'int' object does not support item assignment" in str(err_info.value)

    # dict with nested dict with common key
    # pass because can use non dict to overwrite dict
    d = dict(v=dict(x=0))
    v = dict(v=1)
    got = update_nested_dict(d, v)
    expected = dict(v=1)
    assert got == expected

    # dict with nested dict with common key
    # overwrite a value
    d = dict(v=dict(x=0, y=1))
    v = dict(v=dict(x=1))
    got = update_nested_dict(d, v)
    expected = dict(v=dict(x=1, y=1))
    assert got == expected

    # dict with nested dict with common key
    # add a value
    d = dict(v=dict(x=0, y=1))
    v = dict(v=dict(z=1))
    got = update_nested_dict(d, v)
    expected = dict(v=dict(x=0, y=1, z=1))
    assert got == expected


class TestLoadConfigs:

    def test_single_config(self):

        with open("config/unpaired_labeled_ddf.yaml") as file:
            expected = yaml.load(file, Loader=yaml.FullLoader)
        got = load_configs("config/unpaired_labeled_ddf.yaml")
        assert got == expected

    def test_multiple_configs(self):

        with open("config/unpaired_labeled_ddf.yaml") as file:
            expected = yaml.load(file, Loader=yaml.FullLoader)
        got = load_configs(
            config_path=[
                "config/test/ddf.yaml",
                "config/test/unpaired_nifti.yaml",
                "config/test/labeled.yaml",
            ]
        )
        assert got == expected

    def test_outdated_config(self):

        with open("demos/grouped_mr_heart/grouped_mr_heart.yaml") as file:
            expected = yaml.load(file, Loader=yaml.FullLoader)
        got = load_configs("config/test/grouped_mr_heart_v011.yaml")
        assert got == expected
        updated_file_path = "config/test/updated_grouped_mr_heart_v011.yaml"
        assert os.path.isfile(updated_file_path)
        os.remove(updated_file_path)


def test_save():
    """test save by check error and existance of file"""
    # default file name
    with TempDirectory() as tempdir:
        save(config=dict(x=1), out_dir=tempdir.path)
        assert os.path.exists(os.path.join(tempdir.path, "config.yaml"))

    # custom file name
    with TempDirectory() as tempdir:
        save(config=dict(x=1), out_dir=tempdir.path, filename="test.yaml")
        assert os.path.exists(os.path.join(tempdir.path, "test.yaml"))

    # non yaml filename
    with TempDirectory() as tempdir:
        with pytest.raises(AssertionError):
            save(config=dict(x=1), out_dir=tempdir.path, filename="test.txt")


def test_config_sanity_check(caplog):

    """
    Test config_sanity_check by check error messages

    :param caplog: used to check warning message.
    """

    # unknown data type
    with pytest.raises(ValueError) as err_info:
        config_sanity_check(config=dict(dataset=dict(type="type")))
    assert "data type must be paired / unpaired / grouped" in str(err_info.value)

    # unknown data format
    with pytest.raises(ValueError) as err_info:
        config_sanity_check(config=dict(dataset=dict(type="paired", format="format")))
    assert "data format must be nifti / h5" in str(err_info.value)

    # dir is not in data_config
    with pytest.raises(AssertionError):
        config_sanity_check(config=dict(dataset=dict(type="paired", format="h5")))

    # dir doesn't have train/valid/test
    with pytest.raises(AssertionError):
        config_sanity_check(
            config=dict(dataset=dict(type="paired", format="h5", dir=dict()))
        )

    # train/valid/test of dir is not string or list of string
    with pytest.raises(ValueError) as err_info:
        config_sanity_check(
            config=dict(
                dataset=dict(
                    type="paired",
                    format="h5",
                    dir=dict(train=1, valid=None, test=None),
                    labeled=True,
                ),
                train=dict(model=dict(method="ddf")),
            )
        )
    assert "data_dir for mode train must be string or list of strings" in str(
        err_info.value
    )

    # use unlabeled data for conditional model
    with pytest.raises(ValueError) as err_info:
        config_sanity_check(
            config=dict(
                dataset=dict(
                    type="paired",
                    format="h5",
                    dir=dict(train=None, valid=None, test=None),
                    labeled=False,
                ),
                train=dict(
                    method="conditional",
                    loss=dict(),
                    preprocess=dict(),
                    optimizer=dict(name="Adam"),
                ),
            )
        )
    assert "For conditional model, data have to be labeled, got unlabeled data." in str(
        err_info.value
    )

    # check warnings
    # train/valid/test of dir is None
    # all loss weight <= 0
    caplog.clear()  # clear previous log
    config_sanity_check(
        config=dict(
            dataset=dict(
                type="paired",
                format="h5",
                dir=dict(train=None, valid=None, test=None),
                labeled=False,
            ),
            train=dict(
                method="ddf",
                loss=dict(
                    image=dict(name="lncc", weight=0.0),
                    label=dict(name="ssd", weight=0.0),
                    regularization=dict(name="bending", weight=0.0),
                ),
                preprocess=dict(),
                optimizer=dict(name="Adam"),
            ),
        )
    )
    # warning messages can be detected together
    assert "Data directory for train is not defined." in caplog.text
    assert "Data directory for valid is not defined." in caplog.text
    assert "Data directory for test is not defined." in caplog.text
    assert "The image loss weight 0.00 is not positive." in caplog.text
    assert "The label loss weight 0.00 is not positive." in caplog.text
    assert "The regularization loss weight 0.00 is not positive." in caplog.text


1			"""
2			Tests functions in config/parser.py
3			"""
4
5			import os
6
7			import pytest
8			import yaml
9			from testfixtures import TempDirectory
10
11			from deepreg.config.parser import (
12			config_sanity_check,
13			load_configs,
14			save,
15			update_nested_dict,
16			)
17
18
19			def test_update_nested_dict():
20			"""test update_nested_dict by checking outputs values"""
21			# two simple dicts with different keys
22			d = dict(d=1)
23			v = dict(v=0)
24			got = update_nested_dict(d, v)
25			expected = dict(d=1, v=0)
26			assert got == expected
27
28			# two simple dicts with same key
29			d = dict(d=1)
30			v = dict(d=0)
31			got = update_nested_dict(d, v)
32			expected = dict(d=0)
33			assert got == expected
34
35			# dict with nested dict without common key
36			d = dict(d=1)
37			v = dict(v=dict(x=0))
38			got = update_nested_dict(d, v)
39			expected = dict(d=1, v=dict(x=0))
40			assert got == expected
41
42			# dict with nested dict with common key
43			# fail because can not use dict to overwrite non dict values
44			d = dict(v=1)
45			v = dict(v=dict(x=0))
46			with pytest.raises(TypeError) as err_info:
47			update_nested_dict(d, v)
48			assert "'int' object does not support item assignment" in str(err_info.value)
49
50			# dict with nested dict with common key
51			# pass because can use non dict to overwrite dict
52			d = dict(v=dict(x=0))
53			v = dict(v=1)
54			got = update_nested_dict(d, v)
55			expected = dict(v=1)
56			assert got == expected
57
58			# dict with nested dict with common key
59			# overwrite a value
60			d = dict(v=dict(x=0, y=1))
61			v = dict(v=dict(x=1))
62			got = update_nested_dict(d, v)
63			expected = dict(v=dict(x=1, y=1))
64			assert got == expected
65
66			# dict with nested dict with common key
67			# add a value
68			d = dict(v=dict(x=0, y=1))
69			v = dict(v=dict(z=1))
70			got = update_nested_dict(d, v)
71			expected = dict(v=dict(x=0, y=1, z=1))
72			assert got == expected
73
74
75			class TestLoadConfigs:
			0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
76			def test_single_config(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...
77			with open("config/unpaired_labeled_ddf.yaml") as file:
78			expected = yaml.load(file, Loader=yaml.FullLoader)
79			got = load_configs("config/unpaired_labeled_ddf.yaml")
80			assert got == expected
81
82			def test_multiple_configs(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...
83			with open("config/unpaired_labeled_ddf.yaml") as file:
84			expected = yaml.load(file, Loader=yaml.FullLoader)
85			got = load_configs(
86			config_path=[
87			"config/test/ddf.yaml",
88			"config/test/unpaired_nifti.yaml",
89			"config/test/labeled.yaml",
90			]
91			)
92			assert got == expected
93
94			def test_outdated_config(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...
95			with open("demos/grouped_mr_heart/grouped_mr_heart.yaml") as file:
96			expected = yaml.load(file, Loader=yaml.FullLoader)
97			got = load_configs("config/test/grouped_mr_heart_v011.yaml")
98			assert got == expected
99			updated_file_path = "config/test/updated_grouped_mr_heart_v011.yaml"
100			assert os.path.isfile(updated_file_path)
101			os.remove(updated_file_path)
102
103
104			def test_save():
105			"""test save by check error and existance of file"""
106			# default file name
107			with TempDirectory() as tempdir:
108			save(config=dict(x=1), out_dir=tempdir.path)
109			assert os.path.exists(os.path.join(tempdir.path, "config.yaml"))
110
111			# custom file name
112			with TempDirectory() as tempdir:
113			save(config=dict(x=1), out_dir=tempdir.path, filename="test.yaml")
114			assert os.path.exists(os.path.join(tempdir.path, "test.yaml"))
115
116			# non yaml filename
117			with TempDirectory() as tempdir:
118			with pytest.raises(AssertionError):
119			save(config=dict(x=1), out_dir=tempdir.path, filename="test.txt")
120
121
122			def test_config_sanity_check(caplog):
			0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report "caplog" missing in parameter type documentation Loading history...
123			"""
124			Test config_sanity_check by check error messages
125
126			:param caplog: used to check warning message.
127			"""
128
129			# unknown data type
130			with pytest.raises(ValueError) as err_info:
131			config_sanity_check(config=dict(dataset=dict(type="type")))
132			assert "data type must be paired / unpaired / grouped" in str(err_info.value)
133
134			# unknown data format
135			with pytest.raises(ValueError) as err_info:
136			config_sanity_check(config=dict(dataset=dict(type="paired", format="format")))
137			assert "data format must be nifti / h5" in str(err_info.value)
138
139			# dir is not in data_config
140			with pytest.raises(AssertionError):
141			config_sanity_check(config=dict(dataset=dict(type="paired", format="h5")))
142
143			# dir doesn't have train/valid/test
144			with pytest.raises(AssertionError):
145			config_sanity_check(
146			config=dict(dataset=dict(type="paired", format="h5", dir=dict()))
147			)
148
149			# train/valid/test of dir is not string or list of string
150			with pytest.raises(ValueError) as err_info:
151			config_sanity_check(
152			config=dict(
153			dataset=dict(
154			type="paired",
155			format="h5",
156			dir=dict(train=1, valid=None, test=None),
157			labeled=True,
158			),
159			train=dict(model=dict(method="ddf")),
160			)
161			)
162			assert "data_dir for mode train must be string or list of strings" in str(
163			err_info.value
164			)
165
166			# use unlabeled data for conditional model
167			with pytest.raises(ValueError) as err_info:
168			config_sanity_check(
169			config=dict(
170			dataset=dict(
171			type="paired",
172			format="h5",
173			dir=dict(train=None, valid=None, test=None),
174			labeled=False,
175			),
176			train=dict(
177			method="conditional",
178			loss=dict(),
179			preprocess=dict(),
180			optimizer=dict(name="Adam"),
181			),
182			)
183			)
184			assert "For conditional model, data have to be labeled, got unlabeled data." in str(
185			err_info.value
186			)
187
188			# check warnings
189			# train/valid/test of dir is None
190			# all loss weight <= 0
191			caplog.clear() # clear previous log
192			config_sanity_check(
193			config=dict(
194			dataset=dict(
195			type="paired",
196			format="h5",
197			dir=dict(train=None, valid=None, test=None),
198			labeled=False,
199			),
200			train=dict(
201			method="ddf",
202			loss=dict(
203			image=dict(name="lncc", weight=0.0),
204			label=dict(name="ssd", weight=0.0),
205			regularization=dict(name="bending", weight=0.0),
206			),
207			preprocess=dict(),
208			optimizer=dict(name="Adam"),
209			),
210			)
211			)
212			# warning messages can be detected together
213			assert "Data directory for train is not defined." in caplog.text
214			assert "Data directory for valid is not defined." in caplog.text
215			assert "Data directory for test is not defined." in caplog.text
216			assert "The image loss weight 0.00 is not positive." in caplog.text
217			assert "The label loss weight 0.00 is not positive." in caplog.text
218			assert "The regularization loss weight 0.00 is not positive." in caplog.text
219

DeepRegNet / DeepReg

Pull Request — main (#651)

test_config_sanity_check() C

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Duplication

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How to fix Long Method

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