test.unit.test_config_parser.TestLoadConfigs.test_multiple_configs() - Code Metrics - Inspection of "709 wandb support" - DeepRegNet/DeepReg - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Pull Request — main (#756)

unknown

created 2021-04-19 07:41 UTC

test.unit.test_config_parser.TestLoadConfigs.test_multiple_configs() A

↳ Parent: Project

Complexity

Conditions

Size

Total Lines	11
Code Lines	9

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	9
dl	0
loc	11
rs	9.95
c	0
b	0
f	0
cc	2
nop	1

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

import os

import pytest
import yaml
from testfixtures import TempDirectory

from deepreg.config.parser import (
    config_sanity_check,
    has_wandb_callback,
    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")


class TestConfigSanityCheck:
    def test_cond_err(self):
        """Test error message 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)
        )
<<<<<<< HEAD
=======
    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


@pytest.mark.parametrize(
    """test_dict, expect""", [[{"wandb": True}, True], [{"random": False}, False]]
)
def test_has_wandb_callback(test_dict, expect):
    """
    Testing whether function returns expected value
    from has_wandb_callback
    """
    get = has_wandb_callback(test_dict)
    assert get == expect
>>>>>>> 6448de8c2388756a84bd8c33fa35b3176f09c1c7


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			has_wandb_callback,
14			load_configs,
15			save,
16			update_nested_dict,
17			)
18
19
20			def test_update_nested_dict():
21			"""test update_nested_dict by checking outputs values"""
22			# two simple dicts with different keys
23			d = dict(d=1)
24			v = dict(v=0)
25			got = update_nested_dict(d, v)
26			expected = dict(d=1, v=0)
27			assert got == expected
28
29			# two simple dicts with same key
30			d = dict(d=1)
31			v = dict(d=0)
32			got = update_nested_dict(d, v)
33			expected = dict(d=0)
34			assert got == expected
35
36			# dict with nested dict without common key
37			d = dict(d=1)
38			v = dict(v=dict(x=0))
39			got = update_nested_dict(d, v)
40			expected = dict(d=1, v=dict(x=0))
41			assert got == expected
42
43			# dict with nested dict with common key
44			# fail because can not use dict to overwrite non dict values
45			d = dict(v=1)
46			v = dict(v=dict(x=0))
47			with pytest.raises(TypeError) as err_info:
48			update_nested_dict(d, v)
49			assert "'int' object does not support item assignment" in str(err_info.value)
50
51			# dict with nested dict with common key
52			# pass because can use non dict to overwrite dict
53			d = dict(v=dict(x=0))
54			v = dict(v=1)
55			got = update_nested_dict(d, v)
56			expected = dict(v=1)
57			assert got == expected
58
59			# dict with nested dict with common key
60			# overwrite a value
61			d = dict(v=dict(x=0, y=1))
62			v = dict(v=dict(x=1))
63			got = update_nested_dict(d, v)
64			expected = dict(v=dict(x=1, y=1))
65			assert got == expected
66
67			# dict with nested dict with common key
68			# add a value
69			d = dict(v=dict(x=0, y=1))
70			v = dict(v=dict(z=1))
71			got = update_nested_dict(d, v)
72			expected = dict(v=dict(x=0, y=1, z=1))
73			assert got == expected
74
75
76			class TestLoadConfigs:
77			def test_single_config(self):
78			with open("config/unpaired_labeled_ddf.yaml") as file:
79			expected = yaml.load(file, Loader=yaml.FullLoader)
80			got = load_configs("config/unpaired_labeled_ddf.yaml")
81			assert got == expected
82
83			def test_multiple_configs(self):
84			with open("config/unpaired_labeled_ddf.yaml") as file:
85			expected = yaml.load(file, Loader=yaml.FullLoader)
86			got = load_configs(
87			config_path=[
88			"config/test/ddf.yaml",
89			"config/test/unpaired_nifti.yaml",
90			"config/test/labeled.yaml",
91			]
92			)
93			assert got == expected
94
95			def test_outdated_config(self):
96			with open("demos/grouped_mr_heart/grouped_mr_heart.yaml") as file:
97			expected = yaml.load(file, Loader=yaml.FullLoader)
98			got = load_configs("config/test/grouped_mr_heart_v011.yaml")
99			assert got == expected
100			updated_file_path = "config/test/updated_grouped_mr_heart_v011.yaml"
101			assert os.path.isfile(updated_file_path)
102			os.remove(updated_file_path)
103
104
105			def test_save():
106			"""test save by check error and existance of file"""
107			# default file name
108			with TempDirectory() as tempdir:
109			save(config=dict(x=1), out_dir=tempdir.path)
110			assert os.path.exists(os.path.join(tempdir.path, "config.yaml"))
111
112			# custom file name
113			with TempDirectory() as tempdir:
114			save(config=dict(x=1), out_dir=tempdir.path, filename="test.yaml")
115			assert os.path.exists(os.path.join(tempdir.path, "test.yaml"))
116
117			# non yaml filename
118			with TempDirectory() as tempdir:
119			with pytest.raises(AssertionError):
120			save(config=dict(x=1), out_dir=tempdir.path, filename="test.txt")
121
122
123			class TestConfigSanityCheck:
124			def test_cond_err(self):
125			"""Test error message for conditional model."""
126			with pytest.raises(ValueError) as err_info:
127			config_sanity_check(
128			config=dict(
129			dataset=dict(
130			type="paired",
131			format="h5",
132			dir=dict(train=None, valid=None, test=None),
133			labeled=False,
134			),
135			train=dict(
136			method="conditional",
137			loss=dict(),
138			preprocess=dict(),
139			optimizer=dict(name="Adam"),
140			),
141			)
142			)
143			assert (
144			"For conditional model, data have to be labeled, got unlabeled data."
145			in str(err_info.value)
146			)
147			<<<<<<< HEAD
148			=======
149			assert "data_dir for mode train must be string or list of strings" in str(
150			err_info.value
151			)
152
153			# use unlabeled data for conditional model
154			with pytest.raises(ValueError) as err_info:
155			config_sanity_check(
156			config=dict(
157			dataset=dict(
158			type="paired",
159			format="h5",
160			dir=dict(train=None, valid=None, test=None),
161			labeled=False,
162			),
163			train=dict(
164			method="conditional",
165			loss=dict(),
166			preprocess=dict(),
167			optimizer=dict(name="Adam"),
168			),
169			)
170			)
171			assert "For conditional model, data have to be labeled, got unlabeled data." in str(
172			err_info.value
173			)
174
175			# check warnings
176			# train/valid/test of dir is None
177			# all loss weight <= 0
178			caplog.clear() # clear previous log
179			config_sanity_check(
180			config=dict(
181			dataset=dict(
182			type="paired",
183			format="h5",
184			dir=dict(train=None, valid=None, test=None),
185			labeled=False,
186			),
187			train=dict(
188			method="ddf",
189			loss=dict(
190			image=dict(name="lncc", weight=0.0),
191			label=dict(name="ssd", weight=0.0),
192			regularization=dict(name="bending", weight=0.0),
193			),
194			preprocess=dict(),
195			optimizer=dict(name="Adam"),
196			),
197			)
198			)
199			# warning messages can be detected together
200			assert "Data directory for train is not defined." in caplog.text
201			assert "Data directory for valid is not defined." in caplog.text
202			assert "Data directory for test is not defined." in caplog.text
203
204
205			@pytest.mark.parametrize(
206			"""test_dict, expect""", [[{"wandb": True}, True], [{"random": False}, False]]
207			)
208			def test_has_wandb_callback(test_dict, expect):
209			"""
210			Testing whether function returns expected value
211			from has_wandb_callback
212			"""
213			get = has_wandb_callback(test_dict)
214			assert get == expect
215			>>>>>>> 6448de8c2388756a84bd8c33fa35b3176f09c1c7
216

DeepRegNet / DeepReg

Pull Request — main (#756)

test.unit.test_config_parser.TestLoadConfigs.test_multiple_configs() A

Complexity

Size

Duplication

Importance

Duplication Side-by-Side

Filter issues like