test.unit.test_interface.test_file_loader() - Code Metrics - Inspection of "Merge pull request #675 from DeepRegNet/672-add-my..." - DeepRegNet/DeepReg - Measure and Improve Code Quality continuously with Scrutinizer

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Push — main ( 0c57ec...f6b5bf )

by Yunguan

created 2021-03-06 15:41 UTC

test.unit.test_interface.test_file_loader() C

↳ Parent: test.unit.test_interface

Complexity

Conditions

Size

Total Lines	53
Code Lines	36

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	36
dl	0
loc	53
rs	5.4
c	0
b	0
f	0
cc	11
nop	0

How to fix Long Method Complexity

# coding=utf-8

"""
Tests for deepreg/dataset/loader/interface.py
"""
from test.unit.util import is_equal_np

import numpy as np
import pytest

from deepreg.dataset.loader.interface import (
    AbstractPairedDataLoader,
    AbstractUnpairedDataLoader,
    DataLoader,
    FileLoader,
    GeneratorDataLoader,
)
from deepreg.dataset.loader.nifti_loader import NiftiFileLoader
from deepreg.dataset.loader.paired_loader import PairedDataLoader
from deepreg.dataset.loader.util import normalize_array


class TestDataLoader:

    @pytest.mark.parametrize(
        "labeled,num_indices,sample_label,seed",
        [
            (True, 1, "all", 0),
            (False, 1, "all", 0),
            (None, 1, "all", 0),
            (True, 1, "sample", 0),
            (True, 1, "all", 0),
            (True, 1, None, 0),
            (True, 1, "sample", None),
        ],

    )
    def test_init(self, labeled, num_indices, sample_label, seed):
        """
        Test init function of DataLoader class
        :param labeled: bool
        :param num_indices: int
        :param sample_label: str
        :param seed: float/int/None
        :return:
        """
        DataLoader(
            labeled=labeled,
            num_indices=num_indices,
            sample_label=sample_label,
            seed=seed,
        )

        data_loader = DataLoader(
            labeled=labeled,
            num_indices=num_indices,
            sample_label=sample_label,
            seed=seed,
        )

        with pytest.raises(NotImplementedError):
            data_loader.moving_image_shape
class SomeClass:
    def __init__(self):
        self._x = 5

    def squared(self):
        return self._x * self._x

some_class = SomeClass()
some_class.squared()        # Flagged, as the return value is not used
print(some_class.squared()) # Ok
        with pytest.raises(NotImplementedError):
            data_loader.fixed_image_shape
class SomeClass:
    def __init__(self):
        self._x = 5

    def squared(self):
        return self._x * self._x

some_class = SomeClass()
some_class.squared()        # Flagged, as the return value is not used
print(some_class.squared()) # Ok
        with pytest.raises(NotImplementedError):
            data_loader.num_samples
class SomeClass:
    def __init__(self):
        self._x = 5

    def squared(self):
        return self._x * self._x

some_class = SomeClass()
some_class.squared()        # Flagged, as the return value is not used
print(some_class.squared()) # Ok
        with pytest.raises(NotImplementedError):
            data_loader.get_dataset()

        data_loader.close()

    @pytest.mark.parametrize(
        "labeled,moving_shape,fixed_shape,batch_size,data_augmentation",
        [
            (True, (9, 9, 9), (9, 9, 9), 1, {}),
            (
                True,
                (9, 9, 9),
                (15, 15, 15),
                1,
                {"data_augmentation": {"name": "affine"}},
            ),
            (
                True,
                (9, 9, 9),
                (15, 15, 15),
                1,
                {
                    "data_augmentation": [
                        {"name": "affine"},
                        {
                            "name": "ddf",
                            "field_strength": 1,
                            "low_res_size": (3, 3, 3),
                        },

                    ],
                },
            ),
        ],
    )
    def test_get_dataset_and_preprocess(
        self, labeled, moving_shape, fixed_shape, batch_size, data_augmentation

    ):
        """
        Test get_transforms() function. For that, an Abstract Data Loader is created
        only to set the moving  and fixed shapes that are used in get_transforms().
        Here we test that the get_transform() returns a function and the shape of
        the output of this function. See test_preprocess.py for more testing regarding
        the concrete params.

        :param labeled: bool
        :param moving_shape: tuple
        :param fixed_shape: tuple
        :param batch_size: int
        :param data_augmentation: dict
        :return:
        """
        data_dir_path = [
            "data/test/nifti/paired/train",
            "data/test/nifti/paired/test",
        ]
        common_args = dict(
            file_loader=NiftiFileLoader, labeled=True, sample_label="all", seed=None
        )

        data_loader = PairedDataLoader(
            data_dir_paths=data_dir_path,
            fixed_image_shape=fixed_shape,
            moving_image_shape=moving_shape,
            **common_args,
        )

        dataset = data_loader.get_dataset_and_preprocess(
            training=True,
            batch_size=batch_size,
            repeat=True,
            shuffle_buffer_num_batch=1,
            **data_augmentation,
        )

        for outputs in dataset.take(1):
            assert (
                outputs["moving_image"].shape
                == (batch_size,) + data_loader.moving_image_shape
            )
            assert (
                outputs["fixed_image"].shape
                == (batch_size,) + data_loader.fixed_image_shape
            )
            assert (
                outputs["moving_label"].shape
                == (batch_size,) + data_loader.moving_image_shape
            )
            assert (
                outputs["fixed_label"].shape
                == (batch_size,) + data_loader.fixed_image_shape
            )


def test_abstract_paired_data_loader():
    """
    Test the functions in AbstractPairedDataLoader
    """
    moving_image_shape = (8, 8, 4)
    fixed_image_shape = (6, 6, 4)

    # test init invalid shape
    with pytest.raises(ValueError) as err_info:
        AbstractPairedDataLoader(
            moving_image_shape=(2, 2),
            fixed_image_shape=(3, 3),
            labeled=True,
            sample_label="sample",
        )
    assert "moving_image_shape and fixed_image_shape have length of three" in str(
        err_info.value
    )

    # test init valid shapes
    data_loader = AbstractPairedDataLoader(
        moving_image_shape=moving_image_shape,
        fixed_image_shape=fixed_image_shape,
        labeled=True,
        sample_label="sample",
    )

    # test properties
    assert data_loader.num_indices == 2
    assert data_loader.moving_image_shape == moving_image_shape
    assert data_loader.fixed_image_shape == fixed_image_shape
    assert data_loader.num_samples is None


def test_abstract_unpaired_data_loader():
    """
    Test the functions in AbstractUnpairedDataLoader
    """
    image_shape = (8, 8, 4)

    # test init invalid shape
    with pytest.raises(ValueError) as err_info:
        AbstractUnpairedDataLoader(
            image_shape=(2, 2), labeled=True, sample_label="sample"
        )
    assert "image_shape has to be length of three" in str(err_info.value)

    # test init valid shapes
    data_loader = AbstractUnpairedDataLoader(
        image_shape=image_shape, labeled=True, sample_label="sample"
    )

    # test properties
    assert data_loader.num_indices == 3
    assert data_loader.moving_image_shape == image_shape
    assert data_loader.fixed_image_shape == image_shape
    assert data_loader.num_samples is None


def test_generator_data_loader(caplog):

    """
    Test the functions in GeneratorDataLoader
    :param caplog: used to check warning message.
    """
    generator = GeneratorDataLoader(labeled=True, num_indices=1, sample_label="all")

    # test properties
    assert generator.loader_moving_image is None
    assert generator.loader_moving_image is None
    assert generator.loader_moving_image is None
    assert generator.loader_moving_image is None

    # not implemented properties / functions
    with pytest.raises(NotImplementedError):
        generator.sample_index_generator()

    # implemented functions
    # test get_Dataset
    dummy_array = np.random.random(size=(100, 100, 100)).astype(np.float32)
    # for unlabeled data
    # mock generator
    sequence = [
        dict(
            moving_image=dummy_array,
            fixed_image=dummy_array,
            moving_label=dummy_array,
            fixed_label=dummy_array,
            indices=[1],
        )
        for i in range(3)
    ]

    def mock_generator():
        for el in sequence:
            yield el

    # inputs, no error means passed
    generator.data_generator = mock_generator
    dataset = generator.get_dataset()

    # check dataset output
    expected = dict(
        moving_image=dummy_array,
        fixed_image=dummy_array,
        moving_label=dummy_array,
        fixed_label=dummy_array,
        indices=[1],
    )
    for got in list(dataset.as_numpy_iterator()):
        assert all(is_equal_np(got[key], expected[key]) for key in expected.keys())


    # for unlabeled data
    generator_unlabeled = GeneratorDataLoader(
        labeled=False, num_indices=1, sample_label="all"
    )

    sequence = [
        dict(moving_image=dummy_array, fixed_image=dummy_array, indices=[1])
        for i in range(3)
    ]

    # inputs, no error means passed
    generator_unlabeled.data_generator = mock_generator
    dataset = generator_unlabeled.get_dataset()

    # check dataset output
    expected = dict(moving_image=dummy_array, fixed_image=dummy_array, indices=[1])
    for got in list(dataset.as_numpy_iterator()):
        assert all(is_equal_np(got[key], expected[key]) for key in expected.keys())


    # test data_generator
    # create mock data loader and sample index generator
    class MockDataLoader:

        def __init__(self, **kwargs):

            super().__init__(**kwargs)

        def get_data(index):
class SomeClass:
    def some_method(self):
        # ... do something
            return dummy_array

    def mock_sample_index_generator():
        return [[[1], [1], [1]]]

    generator = GeneratorDataLoader(labeled=True, num_indices=1, sample_label="all")
    generator.sample_index_generator = mock_sample_index_generator
    generator.loader_moving_image = MockDataLoader
    generator.loader_fixed_image = MockDataLoader
    generator.loader_moving_label = MockDataLoader
    generator.loader_fixed_label = MockDataLoader

    # check data generator output
    got = next(generator.data_generator())

    expected = dict(
        moving_image=normalize_array(dummy_array),
        fixed_image=normalize_array(dummy_array),
        moving_label=dummy_array,
        fixed_label=dummy_array,
        indices=np.asarray([1] + [0], dtype=np.float32),
    )
    assert all(is_equal_np(got[key], expected[key]) for key in expected.keys())


    # test validate_images_and_labels
    with pytest.raises(ValueError) as err_info:
        generator.validate_images_and_labels(
            fixed_image=None,
            moving_image=dummy_array,
            moving_label=None,
            fixed_label=None,
            image_indices=[1],
        )
    assert "moving image and fixed image must not be None" in str(err_info.value)
    with pytest.raises(ValueError) as err_info:
        generator.validate_images_and_labels(
            fixed_image=dummy_array,
            moving_image=dummy_array,
            moving_label=dummy_array,
            fixed_label=None,
            image_indices=[1],
        )
    assert "moving label and fixed label must be both None or non-None" in str(
        err_info.value
    )
    with pytest.raises(ValueError) as err_info:
        generator.validate_images_and_labels(
            fixed_image=dummy_array,
            moving_image=dummy_array + 1.0,
            moving_label=None,
            fixed_label=None,
            image_indices=[1],
        )
    assert "Sample [1]'s moving_image's values are not between [0, 1]" in str(
        err_info.value
    )
    with pytest.raises(ValueError) as err_info:
        generator.validate_images_and_labels(
            fixed_image=dummy_array,
            moving_image=np.random.random(size=(100, 100)),
            moving_label=None,
            fixed_label=None,
            image_indices=[1],
        )
    assert "Sample [1]'s moving_image' shape should be 3D. " in str(err_info.value)
    with pytest.raises(ValueError) as err_info:
        generator.validate_images_and_labels(
            fixed_image=dummy_array,
            moving_image=dummy_array,
            moving_label=np.random.random(size=(100, 100)),
            fixed_label=dummy_array,
            image_indices=[1],
        )
    assert "Sample [1]'s moving_label' shape should be 3D or 4D. " in str(
        err_info.value
    )
    with pytest.raises(ValueError) as err_info:
        generator.validate_images_and_labels(
            fixed_image=dummy_array,
            moving_image=dummy_array,
            moving_label=np.random.random(size=(100, 100, 100, 3)),
            fixed_label=np.random.random(size=(100, 100, 100, 4)),
            image_indices=[1],
        )
    assert (
        "Sample [1]'s moving image and fixed image have different numbers of labels."
        in str(err_info.value)
    )

    # warning
    caplog.clear()  # clear previous log
    generator.validate_images_and_labels(
        fixed_image=dummy_array,
        moving_image=dummy_array,
        moving_label=np.random.random(size=(100, 100, 90)),
        fixed_label=dummy_array,
        image_indices=[1],
    )
    assert "Sample [1]'s moving image and label have different shapes. " in caplog.text
    caplog.clear()  # clear previous log
    generator.validate_images_and_labels(
        fixed_image=dummy_array,
        moving_image=dummy_array,
        moving_label=dummy_array,
        fixed_label=np.random.random(size=(100, 100, 90)),
        image_indices=[1],
    )
    assert "Sample [1]'s fixed image and label have different shapes. " in caplog.text

    # test sample_image_label method
    # for unlabeled input data
    got = next(
        generator.sample_image_label(
            fixed_image=dummy_array,
            moving_image=dummy_array,
            moving_label=None,
            fixed_label=None,
            image_indices=[1],
        )
    )
    expected = dict(
        moving_image=dummy_array,
        fixed_image=dummy_array,
        indices=np.asarray([1] + [-1], dtype=np.float32),
    )
    assert all(is_equal_np(got[key], expected[key]) for key in expected.keys())


    # for data with one label
    got = next(
        generator.sample_image_label(
            fixed_image=dummy_array,
            moving_image=dummy_array,
            moving_label=dummy_array,
            fixed_label=dummy_array,
            image_indices=[1],
        )
    )
    expected = dict(
        moving_image=dummy_array,
        fixed_image=dummy_array,
        moving_label=dummy_array,
        fixed_label=dummy_array,
        indices=np.asarray([1] + [0], dtype=np.float32),
    )
    assert all(is_equal_np(got[key], expected[key]) for key in expected.keys())


    # for data with multiple labels
    dummy_labels = np.random.random(size=(100, 100, 100, 3))
    got = generator.sample_image_label(
        fixed_image=dummy_array,
        moving_image=dummy_array,
        moving_label=dummy_labels,
        fixed_label=dummy_labels,
        image_indices=[1],
    )
    for label_index in range(dummy_labels.shape[3]):
        got_iter = next(got)
        expected = dict(
            moving_image=dummy_array,
            fixed_image=dummy_array,
            moving_label=dummy_labels[..., label_index],
            fixed_label=dummy_labels[..., label_index],
            indices=np.asarray([1] + [label_index], dtype=np.float32),
        )
        assert all(is_equal_np(got_iter[key], expected[key]) for key in expected.keys())



def test_file_loader():
    """
    Test the functions in FileLoader
    """
    # init, no error means passed
    loader_grouped = FileLoader(
        dir_paths=["/path/grouped_loader/"], name="grouped_loader", grouped=True
    )
    loader_ungrouped = FileLoader(
        dir_paths=["/path/ungrouped_loader/"], name="ungrouped_loader", grouped=False
    )

    # init fails with repeated paths
    with pytest.raises(ValueError) as err_info:
        FileLoader(
            dir_paths=["/path/ungrouped_loader/", "/path/ungrouped_loader/"],
            name="ungrouped_loader",
            grouped=False,
        )
    assert "dir_paths have repeated elements" in str(err_info.value)

    # not implemented properties / functions
    with pytest.raises(NotImplementedError):
        loader_grouped.set_data_structure()
    with pytest.raises(NotImplementedError):
        loader_grouped.set_group_structure()
    with pytest.raises(NotImplementedError):
        loader_grouped.get_data(1)
    with pytest.raises(NotImplementedError):
        loader_grouped.get_data_ids()
    with pytest.raises(NotImplementedError):
        loader_grouped.get_num_images()
    with pytest.raises(NotImplementedError):
        loader_grouped.close()

    # test grouped file loader functions
    assert loader_grouped.group_struct is None

    # create mock group structure with nested list
    loader_grouped.group_struct = [[1, 2], [3, 4], [5, 6]]
    assert loader_grouped.get_num_groups() == 3
    assert loader_grouped.get_num_images_per_group() == [2, 2, 2]
    with pytest.raises(ValueError) as err_info:
        loader_grouped.group_struct = [[], [3, 4], [5, 6]]
        loader_grouped.get_num_images_per_group()
    assert "Groups of ID [0, 2, 2] are empty." in str(err_info.value)

    # test ungrouped file loader
    assert loader_ungrouped.group_struct is None
    with pytest.raises(AssertionError):
        loader_ungrouped.get_num_groups()
    with pytest.raises(AssertionError):
        loader_ungrouped.get_num_images_per_group()


1			# coding=utf-8
2
3			"""
4			Tests for deepreg/dataset/loader/interface.py
5			"""
6			from test.unit.util import is_equal_np
7
8			import numpy as np
9			import pytest
10
11			from deepreg.dataset.loader.interface import (
12			AbstractPairedDataLoader,
13			AbstractUnpairedDataLoader,
14			DataLoader,
15			FileLoader,
16			GeneratorDataLoader,
17			)
18			from deepreg.dataset.loader.nifti_loader import NiftiFileLoader
19			from deepreg.dataset.loader.paired_loader import PairedDataLoader
20			from deepreg.dataset.loader.util import normalize_array
21
22
23			class TestDataLoader:
			0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
24			@pytest.mark.parametrize(
25			"labeled,num_indices,sample_label,seed",
26			[
27			(True, 1, "all", 0),
28			(False, 1, "all", 0),
29			(None, 1, "all", 0),
30			(True, 1, "sample", 0),
31			(True, 1, "all", 0),
32			(True, 1, None, 0),
33			(True, 1, "sample", None),
34			],
			0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report "labeled, num_indices, sample_label, seed" missing in parameter type documentation Loading history... introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Redundant returns documentation Loading history...
35			)
36			def test_init(self, labeled, num_indices, sample_label, seed):
37			"""
38			Test init function of DataLoader class
39			:param labeled: bool
40			:param num_indices: int
41			:param sample_label: str
42			:param seed: float/int/None
43			:return:
44			"""
45			DataLoader(
46			labeled=labeled,
47			num_indices=num_indices,
48			sample_label=sample_label,
49			seed=seed,
50			)
51
52			data_loader = DataLoader(
53			labeled=labeled,
54			num_indices=num_indices,
55			sample_label=sample_label,
56			seed=seed,
57			)
58
59			with pytest.raises(NotImplementedError):
60			data_loader.moving_image_shape
			0 ignored issues – show Unused Code introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report This statement seems to have no effect and could be removed. This issue is typically triggered when a function that does not have side-effects is called and the return value is discarded: class SomeClass: def __init__(self): self._x = 5 def squared(self): return self._x * self._x some_class = SomeClass() some_class.squared() # Flagged, as the return value is not used print(some_class.squared()) # Ok Loading history...
61			with pytest.raises(NotImplementedError):
62			data_loader.fixed_image_shape
			0 ignored issues – show Unused Code introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report This statement seems to have no effect and could be removed. This issue is typically triggered when a function that does not have side-effects is called and the return value is discarded: class SomeClass: def __init__(self): self._x = 5 def squared(self): return self._x * self._x some_class = SomeClass() some_class.squared() # Flagged, as the return value is not used print(some_class.squared()) # Ok Loading history...
63			with pytest.raises(NotImplementedError):
64			data_loader.num_samples
			0 ignored issues – show Unused Code introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report This statement seems to have no effect and could be removed. This issue is typically triggered when a function that does not have side-effects is called and the return value is discarded: class SomeClass: def __init__(self): self._x = 5 def squared(self): return self._x * self._x some_class = SomeClass() some_class.squared() # Flagged, as the return value is not used print(some_class.squared()) # Ok Loading history...
65			with pytest.raises(NotImplementedError):
66			data_loader.get_dataset()
67
68			data_loader.close()
69
70			@pytest.mark.parametrize(
71			"labeled,moving_shape,fixed_shape,batch_size,data_augmentation",
72			[
73			(True, (9, 9, 9), (9, 9, 9), 1, {}),
74			(
75			True,
76			(9, 9, 9),
77			(15, 15, 15),
78			1,
79			{"data_augmentation": {"name": "affine"}},
80			),
81			(
82			True,
83			(9, 9, 9),
84			(15, 15, 15),
85			1,
86			{
87			"data_augmentation": [
88			{"name": "affine"},
89			{
90			"name": "ddf",
91			"field_strength": 1,
92			"low_res_size": (3, 3, 3),
93			},
			0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report "batch_size, data_augmentation, fixed_shape, labeled, moving_shape" missing in parameter type documentation Loading history... introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Redundant returns documentation Loading history...
94			],
95			},
96			),
97			],
98			)
99			def test_get_dataset_and_preprocess(
100			self, labeled, moving_shape, fixed_shape, batch_size, data_augmentation
			0 ignored issues – show Unused Code introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report The argument `labeled` seems to be unused. Loading history...
101			):
102			"""
103			Test get_transforms() function. For that, an Abstract Data Loader is created
104			only to set the moving and fixed shapes that are used in get_transforms().
105			Here we test that the get_transform() returns a function and the shape of
106			the output of this function. See test_preprocess.py for more testing regarding
107			the concrete params.
108
109			:param labeled: bool
110			:param moving_shape: tuple
111			:param fixed_shape: tuple
112			:param batch_size: int
113			:param data_augmentation: dict
114			:return:
115			"""
116			data_dir_path = [
117			"data/test/nifti/paired/train",
118			"data/test/nifti/paired/test",
119			]
120			common_args = dict(
121			file_loader=NiftiFileLoader, labeled=True, sample_label="all", seed=None
122			)
123
124			data_loader = PairedDataLoader(
125			data_dir_paths=data_dir_path,
126			fixed_image_shape=fixed_shape,
127			moving_image_shape=moving_shape,
128			**common_args,
129			)
130
131			dataset = data_loader.get_dataset_and_preprocess(
132			training=True,
133			batch_size=batch_size,
134			repeat=True,
135			shuffle_buffer_num_batch=1,
136			**data_augmentation,
137			)
138
139			for outputs in dataset.take(1):
140			assert (
141			outputs["moving_image"].shape
142			== (batch_size,) + data_loader.moving_image_shape
143			)
144			assert (
145			outputs["fixed_image"].shape
146			== (batch_size,) + data_loader.fixed_image_shape
147			)
148			assert (
149			outputs["moving_label"].shape
150			== (batch_size,) + data_loader.moving_image_shape
151			)
152			assert (
153			outputs["fixed_label"].shape
154			== (batch_size,) + data_loader.fixed_image_shape
155			)
156
157
158			def test_abstract_paired_data_loader():
159			"""
160			Test the functions in AbstractPairedDataLoader
161			"""
162			moving_image_shape = (8, 8, 4)
163			fixed_image_shape = (6, 6, 4)
164
165			# test init invalid shape
166			with pytest.raises(ValueError) as err_info:
167			AbstractPairedDataLoader(
168			moving_image_shape=(2, 2),
169			fixed_image_shape=(3, 3),
170			labeled=True,
171			sample_label="sample",
172			)
173			assert "moving_image_shape and fixed_image_shape have length of three" in str(
174			err_info.value
175			)
176
177			# test init valid shapes
178			data_loader = AbstractPairedDataLoader(
179			moving_image_shape=moving_image_shape,
180			fixed_image_shape=fixed_image_shape,
181			labeled=True,
182			sample_label="sample",
183			)
184
185			# test properties
186			assert data_loader.num_indices == 2
187			assert data_loader.moving_image_shape == moving_image_shape
188			assert data_loader.fixed_image_shape == fixed_image_shape
189			assert data_loader.num_samples is None
190
191
192			def test_abstract_unpaired_data_loader():
193			"""
194			Test the functions in AbstractUnpairedDataLoader
195			"""
196			image_shape = (8, 8, 4)
197
198			# test init invalid shape
199			with pytest.raises(ValueError) as err_info:
200			AbstractUnpairedDataLoader(
201			image_shape=(2, 2), labeled=True, sample_label="sample"
202			)
203			assert "image_shape has to be length of three" in str(err_info.value)
204
205			# test init valid shapes
206			data_loader = AbstractUnpairedDataLoader(
207			image_shape=image_shape, labeled=True, sample_label="sample"
208			)
209
210			# test properties
211			assert data_loader.num_indices == 3
212			assert data_loader.moving_image_shape == image_shape
213			assert data_loader.fixed_image_shape == image_shape
214			assert data_loader.num_samples is None
215
216
217			def test_generator_data_loader(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...
218			"""
219			Test the functions in GeneratorDataLoader
220			:param caplog: used to check warning message.
221			"""
222			generator = GeneratorDataLoader(labeled=True, num_indices=1, sample_label="all")
223
224			# test properties
225			assert generator.loader_moving_image is None
226			assert generator.loader_moving_image is None
227			assert generator.loader_moving_image is None
228			assert generator.loader_moving_image is None
229
230			# not implemented properties / functions
231			with pytest.raises(NotImplementedError):
232			generator.sample_index_generator()
233
234			# implemented functions
235			# test get_Dataset
236			dummy_array = np.random.random(size=(100, 100, 100)).astype(np.float32)
237			# for unlabeled data
238			# mock generator
239			sequence = [
240			dict(
241			moving_image=dummy_array,
242			fixed_image=dummy_array,
243			moving_label=dummy_array,
244			fixed_label=dummy_array,
245			indices=[1],
246			)
247			for i in range(3)
248			]
249
250			def mock_generator():
251			for el in sequence:
252			yield el
253
254			# inputs, no error means passed
255			generator.data_generator = mock_generator
256			dataset = generator.get_dataset()
257
258			# check dataset output
259			expected = dict(
260			moving_image=dummy_array,
261			fixed_image=dummy_array,
262			moving_label=dummy_array,
263			fixed_label=dummy_array,
264			indices=[1],
265			)
266			for got in list(dataset.as_numpy_iterator()):
267			assert all(is_equal_np(got[key], expected[key]) for key in expected.keys())
			0 ignored issues – show unused-code introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Consider iterating the dictionary directly instead of calling .keys() Loading history...
268
269			# for unlabeled data
270			generator_unlabeled = GeneratorDataLoader(
271			labeled=False, num_indices=1, sample_label="all"
272			)
273
274			sequence = [
275			dict(moving_image=dummy_array, fixed_image=dummy_array, indices=[1])
276			for i in range(3)
277			]
278
279			# inputs, no error means passed
280			generator_unlabeled.data_generator = mock_generator
281			dataset = generator_unlabeled.get_dataset()
282
283			# check dataset output
284			expected = dict(moving_image=dummy_array, fixed_image=dummy_array, indices=[1])
285			for got in list(dataset.as_numpy_iterator()):
286			assert all(is_equal_np(got[key], expected[key]) for key in expected.keys())
			0 ignored issues – show unused-code introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Consider iterating the dictionary directly instead of calling .keys() Loading history...
287
288			# test data_generator
289			# create mock data loader and sample index generator
290			class MockDataLoader:
			0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
291			def __init__(self, **kwargs):
			0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Useless super delegation in method '__init__' Loading history...
292			super().__init__(**kwargs)
293
294			def get_data(index):
			0 ignored issues – show introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history... Coding Style Best Practice introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Methods should have `self` as first argument. It is a widespread convention and generally a good practice to name the first argument of methods `self`. class SomeClass: def some_method(self): # ... do something Loading history...
295			return dummy_array
296
297			def mock_sample_index_generator():
298			return [[[1], [1], [1]]]
299
300			generator = GeneratorDataLoader(labeled=True, num_indices=1, sample_label="all")
301			generator.sample_index_generator = mock_sample_index_generator
302			generator.loader_moving_image = MockDataLoader
303			generator.loader_fixed_image = MockDataLoader
304			generator.loader_moving_label = MockDataLoader
305			generator.loader_fixed_label = MockDataLoader
306
307			# check data generator output
308			got = next(generator.data_generator())
309
310			expected = dict(
311			moving_image=normalize_array(dummy_array),
312			fixed_image=normalize_array(dummy_array),
313			moving_label=dummy_array,
314			fixed_label=dummy_array,
315			indices=np.asarray([1] + [0], dtype=np.float32),
316			)
317			assert all(is_equal_np(got[key], expected[key]) for key in expected.keys())
			0 ignored issues – show unused-code introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Consider iterating the dictionary directly instead of calling .keys() Loading history...
318
319			# test validate_images_and_labels
320			with pytest.raises(ValueError) as err_info:
321			generator.validate_images_and_labels(
322			fixed_image=None,
323			moving_image=dummy_array,
324			moving_label=None,
325			fixed_label=None,
326			image_indices=[1],
327			)
328			assert "moving image and fixed image must not be None" in str(err_info.value)
329			with pytest.raises(ValueError) as err_info:
330			generator.validate_images_and_labels(
331			fixed_image=dummy_array,
332			moving_image=dummy_array,
333			moving_label=dummy_array,
334			fixed_label=None,
335			image_indices=[1],
336			)
337			assert "moving label and fixed label must be both None or non-None" in str(
338			err_info.value
339			)
340			with pytest.raises(ValueError) as err_info:
341			generator.validate_images_and_labels(
342			fixed_image=dummy_array,
343			moving_image=dummy_array + 1.0,
344			moving_label=None,
345			fixed_label=None,
346			image_indices=[1],
347			)
348			assert "Sample [1]'s moving_image's values are not between [0, 1]" in str(
349			err_info.value
350			)
351			with pytest.raises(ValueError) as err_info:
352			generator.validate_images_and_labels(
353			fixed_image=dummy_array,
354			moving_image=np.random.random(size=(100, 100)),
355			moving_label=None,
356			fixed_label=None,
357			image_indices=[1],
358			)
359			assert "Sample [1]'s moving_image' shape should be 3D. " in str(err_info.value)
360			with pytest.raises(ValueError) as err_info:
361			generator.validate_images_and_labels(
362			fixed_image=dummy_array,
363			moving_image=dummy_array,
364			moving_label=np.random.random(size=(100, 100)),
365			fixed_label=dummy_array,
366			image_indices=[1],
367			)
368			assert "Sample [1]'s moving_label' shape should be 3D or 4D. " in str(
369			err_info.value
370			)
371			with pytest.raises(ValueError) as err_info:
372			generator.validate_images_and_labels(
373			fixed_image=dummy_array,
374			moving_image=dummy_array,
375			moving_label=np.random.random(size=(100, 100, 100, 3)),
376			fixed_label=np.random.random(size=(100, 100, 100, 4)),
377			image_indices=[1],
378			)
379			assert (
380			"Sample [1]'s moving image and fixed image have different numbers of labels."
381			in str(err_info.value)
382			)
383
384			# warning
385			caplog.clear() # clear previous log
386			generator.validate_images_and_labels(
387			fixed_image=dummy_array,
388			moving_image=dummy_array,
389			moving_label=np.random.random(size=(100, 100, 90)),
390			fixed_label=dummy_array,
391			image_indices=[1],
392			)
393			assert "Sample [1]'s moving image and label have different shapes. " in caplog.text
394			caplog.clear() # clear previous log
395			generator.validate_images_and_labels(
396			fixed_image=dummy_array,
397			moving_image=dummy_array,
398			moving_label=dummy_array,
399			fixed_label=np.random.random(size=(100, 100, 90)),
400			image_indices=[1],
401			)
402			assert "Sample [1]'s fixed image and label have different shapes. " in caplog.text
403
404			# test sample_image_label method
405			# for unlabeled input data
406			got = next(
407			generator.sample_image_label(
408			fixed_image=dummy_array,
409			moving_image=dummy_array,
410			moving_label=None,
411			fixed_label=None,
412			image_indices=[1],
413			)
414			)
415			expected = dict(
416			moving_image=dummy_array,
417			fixed_image=dummy_array,
418			indices=np.asarray([1] + [-1], dtype=np.float32),
419			)
420			assert all(is_equal_np(got[key], expected[key]) for key in expected.keys())
			0 ignored issues – show unused-code introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Consider iterating the dictionary directly instead of calling .keys() Loading history...
421
422			# for data with one label
423			got = next(
424			generator.sample_image_label(
425			fixed_image=dummy_array,
426			moving_image=dummy_array,
427			moving_label=dummy_array,
428			fixed_label=dummy_array,
429			image_indices=[1],
430			)
431			)
432			expected = dict(
433			moving_image=dummy_array,
434			fixed_image=dummy_array,
435			moving_label=dummy_array,
436			fixed_label=dummy_array,
437			indices=np.asarray([1] + [0], dtype=np.float32),
438			)
439			assert all(is_equal_np(got[key], expected[key]) for key in expected.keys())
			0 ignored issues – show unused-code introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Consider iterating the dictionary directly instead of calling .keys() Loading history...
440
441			# for data with multiple labels
442			dummy_labels = np.random.random(size=(100, 100, 100, 3))
443			got = generator.sample_image_label(
444			fixed_image=dummy_array,
445			moving_image=dummy_array,
446			moving_label=dummy_labels,
447			fixed_label=dummy_labels,
448			image_indices=[1],
449			)
450			for label_index in range(dummy_labels.shape[3]):
451			got_iter = next(got)
452			expected = dict(
453			moving_image=dummy_array,
454			fixed_image=dummy_array,
455			moving_label=dummy_labels[..., label_index],
456			fixed_label=dummy_labels[..., label_index],
457			indices=np.asarray([1] + [label_index], dtype=np.float32),
458			)
459			assert all(is_equal_np(got_iter[key], expected[key]) for key in expected.keys())
			0 ignored issues – show unused-code introduced 2021-01-26 01:41 UTC by Report Bug Copy Issue Report Consider iterating the dictionary directly instead of calling .keys() Loading history...
460
461
462			def test_file_loader():
463			"""
464			Test the functions in FileLoader
465			"""
466			# init, no error means passed
467			loader_grouped = FileLoader(
468			dir_paths=["/path/grouped_loader/"], name="grouped_loader", grouped=True
469			)
470			loader_ungrouped = FileLoader(
471			dir_paths=["/path/ungrouped_loader/"], name="ungrouped_loader", grouped=False
472			)
473
474			# init fails with repeated paths
475			with pytest.raises(ValueError) as err_info:
476			FileLoader(
477			dir_paths=["/path/ungrouped_loader/", "/path/ungrouped_loader/"],
478			name="ungrouped_loader",
479			grouped=False,
480			)
481			assert "dir_paths have repeated elements" in str(err_info.value)
482
483			# not implemented properties / functions
484			with pytest.raises(NotImplementedError):
485			loader_grouped.set_data_structure()
486			with pytest.raises(NotImplementedError):
487			loader_grouped.set_group_structure()
488			with pytest.raises(NotImplementedError):
489			loader_grouped.get_data(1)
490			with pytest.raises(NotImplementedError):
491			loader_grouped.get_data_ids()
492			with pytest.raises(NotImplementedError):
493			loader_grouped.get_num_images()
494			with pytest.raises(NotImplementedError):
495			loader_grouped.close()
496
497			# test grouped file loader functions
498			assert loader_grouped.group_struct is None
499
500			# create mock group structure with nested list
501			loader_grouped.group_struct = [[1, 2], [3, 4], [5, 6]]
502			assert loader_grouped.get_num_groups() == 3
503			assert loader_grouped.get_num_images_per_group() == [2, 2, 2]
504			with pytest.raises(ValueError) as err_info:
505			loader_grouped.group_struct = [[], [3, 4], [5, 6]]
506			loader_grouped.get_num_images_per_group()
507			assert "Groups of ID [0, 2, 2] are empty." in str(err_info.value)
508
509			# test ungrouped file loader
510			assert loader_ungrouped.group_struct is None
511			with pytest.raises(AssertionError):
512			loader_ungrouped.get_num_groups()
513			with pytest.raises(AssertionError):
514			loader_ungrouped.get_num_images_per_group()
515

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