Unit tests

ome_zarr

img2d()

A ome_zarr.Image object representing a 2D image

Source code in tests/test_ome_zarr.py

@pytest.fixture
def img2d():
    """A `ome_zarr.Image` object representing a 2D image"""
    return ome_zarr.Image('tests/example_data/plate_ones_mip.zarr/B/03/0', name="test")

img3d()

A ome_zarr.Image object representing a 3D image

Source code in tests/test_ome_zarr.py

@pytest.fixture
def img3d():
    """A `ome_zarr.Image` object representing a 3D image"""
    return ome_zarr.Image('tests/example_data/plate_ones.zarr/B/03/0')

imgL()

A ome_zarr.ImageList object with one image

Source code in tests/test_ome_zarr.py

@pytest.fixture
def imgL():
    """A `ome_zarr.ImageList` object with one image"""
    return ome_zarr.ImageList(['tests/example_data/plate_ones_mip.zarr/B/03/0'])

imgL2()

A ome_zarr.ImageList object with two images

Source code in tests/test_ome_zarr.py

@pytest.fixture
def imgL2():
    """A `ome_zarr.ImageList` object with two images"""
    return ome_zarr.ImageList(['tests/example_data/plate_ones_mip.zarr/B/03/0', 'tests/example_data/plate_ones_mip.zarr/B/03/0'])

test_compare_multiscale_dicts()

Test Image._compare_multiscale_dicts.

Source code in tests/test_ome_zarr.py

def test_compare_multiscale_dicts():
    """Test `Image._compare_multiscale_dicts`."""

    datasets = [{'path': 1, 'coordinateTransformations': [{'type': 'scale',
    'scale': [1.0, 0.325, 0.325]}]},
                {'path': 2, 'coordinateTransformations': [{'type': 'scale',
    'scale': [1.0, 0.65, 0.65]}]},
                {'path': 0, 'coordinateTransformations': [{'type': 'scale',
    'scale': [1.0, 0.1625, 0.1625]}]}]

    assert ome_zarr.Image._compare_multiscale_dicts(datasets[0], datasets[0]) == 0
    assert ome_zarr.Image._compare_multiscale_dicts(datasets[0], datasets[1]) == -1
    assert ome_zarr.Image._compare_multiscale_dicts(datasets[1], datasets[2]) == 1

test_constructor(img2d, img3d, tmpdir)

Test ome_zarr.Image object constructor.

Source code in tests/test_ome_zarr.py

def test_constructor(img2d: ome_zarr.Image, img3d: ome_zarr.Image, tmpdir: str):
    """Test `ome_zarr.Image` object constructor."""

    # non-conforming input
    # ... multiple zarr groups
    assert tmpdir.check()
    shutil.copytree('tests/example_data/plate_ones_mip.zarr/B/03/0',
                    str(tmpdir) + '/example_img')
    shutil.copytree('tests/example_data/plate_ones_mip.zarr/B/03/0/labels',
                    str(tmpdir) + '/example_img/labels_copy')
    with pytest.raises(Exception) as e_info:
        ome_zarr.Image(str(tmpdir) + '/example_img')
    shutil.rmtree(str(tmpdir) + '/example_img/labels_copy')
    # ... path without array
    with pytest.raises(Exception) as e_info:
        ome_zarr.Image('tests/example_data/')
    # ... missing omero
    zattr_file = str(tmpdir) + '/example_img/.zattrs'
    shutil.copyfile(zattr_file, zattr_file + '.orig')
    with open(zattr_file) as f:
       zattr = json.load(f)
    del zattr['omero']
    with open(zattr_file, "w") as jsonfile:
        json.dump(zattr, jsonfile, indent=4)
    img_no_omero = ome_zarr.Image(str(tmpdir) + '/example_img')
    assert img_no_omero.channels == [{'label': 'channel-1', 'color': '00FFFF'}, {'label': 'channel-2', 'color': '00FFFF'}]
    shutil.move(zattr_file + '.orig', zattr_file)
    # ... clean up
    shutil.rmtree(str(tmpdir) + '/example_img')

    # 2D image with labels
    assert isinstance(img2d, ome_zarr.Image)
    assert img2d.path == 'tests/example_data/plate_ones_mip.zarr/B/03/0'
    assert img2d.name == 'test'
    assert isinstance(img2d.zarr_group, zarr.Group)
    assert all([isinstance(x, zarr.Array) for x in img2d.array_dict.values()])
    assert img2d.ndim == 4
    assert img2d.label_names == ['organoids']
    assert img2d.table_names == ['FOV_ROI_table']
    assert img2d.axes_unit_image == 'micrometer'
    assert img2d.channel_info_image == 'czyx'
    assert img2d.channel_info_labels == {'organoids': 'zyx'}
    assert img2d.nchannels_image == 2
    assert isinstance(img2d.channels, list)
    assert all([isinstance(img2d.channels[i], dict) for i in range(img2d.nchannels_image)])

    # 3D image without labels
    assert isinstance(img3d, ome_zarr.Image)
    assert img3d.path == 'tests/example_data/plate_ones.zarr/B/03/0'
    assert img3d.name == '0'
    assert isinstance(img3d.zarr_group, zarr.Group)
    assert all([isinstance(x, zarr.Array) for x in img3d.array_dict.values()])
    assert img3d.ndim == 4
    assert img3d.label_names == []
    assert img3d.table_names == ['FOV_ROI_table']
    assert img3d.axes_unit_image == 'micrometer'
    assert img3d.channel_info_image == 'czyx'
    assert img3d.channel_info_labels == {}
    assert img3d.nchannels_image == 2
    assert isinstance(img3d.channels, list)
    assert all([isinstance(img3d.channels[i], dict) for i in range(img3d.nchannels_image)])

test_create_name_plate_A01()

Test ome_zarr.create_name_plate_A01 function.

Source code in tests/test_ome_zarr.py

def test_create_name_plate_A01():
    """Test `ome_zarr.create_name_plate_A01` function."""
    with pytest.raises(Exception) as e_info:
        ome_zarr.create_name_plate_A01(1)
    with pytest.raises(Exception) as e_info:
        ome_zarr.create_name_plate_A01(1, 2, 3)
    assert ome_zarr.create_name_plate_A01(1, 2) == 'A02'
    assert ome_zarr.create_name_plate_A01(3, 4) == 'C04'
    assert ome_zarr.create_name_plate_A01(5, 11) == 'E11'

test_create_name_row_col()

Test ome_zarr.create_name_row_col function.

Source code in tests/test_ome_zarr.py

def test_create_name_row_col():
    """Test `ome_zarr.create_name_row_col` function."""
    with pytest.raises(Exception) as e_info:
        ome_zarr.create_name_row_col(1)
    with pytest.raises(Exception) as e_info:
        ome_zarr.create_name_row_col(1, 2, 3)
    assert ome_zarr.create_name_row_col(1, 2) == '1_2'
    assert ome_zarr.create_name_row_col(3, 4) == '3_4'

test_digest_bounding_box(img2d)

Test Image._digest_bounding_box.

Source code in tests/test_ome_zarr.py

def test_digest_bounding_box(img2d: ome_zarr.Image):
    """Test `Image._digest_bounding_box`."""

    # invalid input
    with pytest.raises(Exception) as e_info: # unknown label
        img2d._digest_bounding_box(label_name='error')
    with pytest.raises(Exception) as e_info: # missing coordinates
        img2d._digest_bounding_box(upper_left_yx=(5, 10))
    with pytest.raises(Exception) as e_info: # wrong dimensions
        img2d._digest_bounding_box(upper_left_yx=(5, 10, 10), size_yx=(1, 1, 1))
    with pytest.raises(Exception) as e_info: # unknown pyramid level
        img2d._digest_bounding_box(upper_left_yx=(5, 10), lower_right_yx=(20, 50), pyramid_level=7)
    with pytest.raises(Exception) as e_info: # unknown coord pyramid level
        img2d._digest_bounding_box(upper_left_yx=(5, 10), lower_right_yx=(20, 50), pyramid_level_coord=7, coordinate_unit='pixel')
    with pytest.raises(Exception) as e_info: # unknown coordinate unit
        img2d._digest_bounding_box(upper_left_yx=(5, 10), lower_right_yx=(20, 50), coordinate_unit = 'error')

    # expected results
    # ... full array
    assert img2d._digest_bounding_box() == [(0, 0), (270, 320)]
    # ... corners from different inputs
    assert img2d._digest_bounding_box(upper_left_yx=(5, 10),
                                      lower_right_yx=(20, 50),
                                      coordinate_unit='pixel') == [(5, 10), (20, 50)]
    assert img2d._digest_bounding_box(upper_left_yx=(5, 10),
                                      size_yx=(15, 40),
                                      coordinate_unit='pixel') == [(5, 10), (20, 50)]
    assert img2d._digest_bounding_box(size_yx=(15, 40),
                                      lower_right_yx=(20, 50),
                                      coordinate_unit='pixel') == [(5, 10), (20, 50)]
    # ... different pyramid levels
    assert img2d._digest_bounding_box(upper_left_yx=(5, 10),
                                      lower_right_yx=(20, 50),
                                      pyramid_level=1,
                                      pyramid_level_coord=2,
                                      coordinate_unit='pixel') == [(10, 20), (40, 100)]
    # ... micrometer coordinates
    s = img2d.get_scale(pyramid_level=1)
    assert img2d._digest_bounding_box(upper_left_yx=(0, 0),
                                      lower_right_yx=(s[-2] * 1000, s[-1] * 1000),
                                      pyramid_level=1,
                                      coordinate_unit='micrometer') == [(0, 0), (1000, 1000)]
    # ... label array
    assert img2d._digest_bounding_box(label_name='organoids') == [(0, 0), (270, 320)]

test_digest_channels_labels(img2d)

Test Image._digest_channels_labels.

Source code in tests/test_ome_zarr.py

def test_digest_channels_labels(img2d: ome_zarr.Image):
    """Test `Image._digest_channels_labels`."""

    # invalid input
    with pytest.raises(Exception) as e_info:
        img2d._digest_channels_labels(None)
    with pytest.raises(Exception) as e_info:
        img2d._digest_channels_labels(['error'])

    # expected results
    assert img2d._digest_channels_labels(['some-label-1']) == [0]
    assert img2d._digest_channels_labels(['some-label-2', 'some-label-1']) == [1, 0]

test_digest_pyramid_level_argument(img2d, img3d)

Test Image._digest_pyramid_level_argument.

Source code in tests/test_ome_zarr.py

def test_digest_pyramid_level_argument(img2d: ome_zarr.Image, img3d: ome_zarr.Image):
    """Test `Image._digest_pyramid_level_argument`."""

    # invalid input
    with pytest.raises(Exception) as e_info:
        img2d._digest_pyramid_level_argument(6)
    with pytest.raises(Exception) as e_info:
        img2d._digest_pyramid_level_argument(None, 'error')

    # 2D image with labels    
    assert img2d._digest_pyramid_level_argument(None) == '2'
    assert img2d._digest_pyramid_level_argument(1, None) == '1'
    assert img2d._digest_pyramid_level_argument(1, 'organoids') == '1'
    assert img2d._digest_pyramid_level_argument('1', 'organoids') == '1'
    assert img2d._digest_pyramid_level_argument(None, 'organoids') == '2'

    # 3D image without labels
    assert img3d._digest_pyramid_level_argument(None) == '2'
    assert img3d._digest_pyramid_level_argument(1) == '1'
    assert img3d._digest_pyramid_level_argument('1', None) == '1'

test_extract_scale_spacings(img2d)

Test Image._extract_scale_spacings.

Source code in tests/test_ome_zarr.py

def test_extract_scale_spacings(img2d: ome_zarr.Image):
    """Test `Image._extract_scale_spacings`."""

    # input with missing axes
    with pytest.raises(Exception) as e_info:
        img2d._extract_scale_spacings({})

    # example input
    assert img2d._extract_scale_spacings(img2d.multiscales_image['datasets'][0]) == [0, [1.0, 1.0, 0.1625, 0.1625]]
    assert img2d._extract_scale_spacings(img2d.multiscales_labels['organoids']['datasets'][1]) == [1, [1.0, 0.325, 0.325]]

    # synthetic input
    assert img2d._extract_scale_spacings(
        {'path': 11, 'coordinateTransformations': [{'scale': [1, 2.0, 3.25]}]}
    ) == [11, [1.0, 2.0, 3.25]]
    assert img2d._extract_scale_spacings(
        {'path': 7, 'coordinateTransformations': [{'scale': [1, 2, 0.5]}]}
    ) == [7, [1.0, 2.0, 0.5]]

test_find_path_of_highest_resolution_level(img2d)

Test Image._find_path_of_highest_resolution_level.

Source code in tests/test_ome_zarr.py

def test_find_path_of_highest_resolution_level(img2d: ome_zarr.Image):
    """Test `Image._find_path_of_highest_resolution_level`."""

    # non-existing label_name
    with pytest.raises(Exception) as e_info:
        img2d._find_path_of_highest_resolution_level(label_name='error')

    # example input
    assert img2d._find_path_of_highest_resolution_level() == '0'
    assert img2d._find_path_of_highest_resolution_level(label_name='organoids') == '0'

test_find_path_of_lowest_level(img2d)

Test Image._find_path_of_lowest_resolution_level.

Source code in tests/test_ome_zarr.py

def test_find_path_of_lowest_level(img2d: ome_zarr.Image):
    """Test `Image._find_path_of_lowest_resolution_level`."""

    # non-existing label_name
    with pytest.raises(Exception) as e_info:
        img2d._find_path_of_lowest_resolution_level(label_name='error')

    # example input
    assert img2d._find_path_of_lowest_resolution_level() == '2'
    assert img2d._find_path_of_lowest_resolution_level(label_name='organoids') == '2'

    # synthetic input
    assert img2d._extract_paths_by_decreasing_resolution(
        [{'path': 0, 'coordinateTransformations': [{'scale': [0.2, 0.2, 0.2]}]},
         {'path': 1, 'coordinateTransformations': [{'scale': [0.1, 0.4, 0.1]}]}
        ]) == ['1', '0']
    assert img2d._extract_paths_by_decreasing_resolution(
        [{'path': 0, 'coordinateTransformations': [{'scale': [0.1, 0.1]}]},
         {'path': 1, 'coordinateTransformations': [{'scale': [0.1, 0.2]}]}
        ]) == ['0', '1']

test_get_array_by_coordinate(img2d, img3d)

Test ome_zarr.Image object get_array_by_coordinate() method.

Source code in tests/test_ome_zarr.py

def test_get_array_by_coordinate(img2d: ome_zarr.Image, img3d: ome_zarr.Image):
    """Test `ome_zarr.Image` object get_array_by_coordinate() method."""

    # invalid input
    with pytest.raises(Exception) as e_info: # unknown label
        img2d.get_array_by_coordinate('error')
    with pytest.raises(Exception) as e_info: # missing coordinates
        img2d.get_array_by_coordinate(upper_left_yx=(5, 10))
    with pytest.raises(Exception) as e_info: # wrong dimensions
        img2d.get_array_by_coordinate(upper_left_yx=(5, 10, 10), size_yx=(1, 1, 1))
    with pytest.raises(Exception) as e_info: # unknown pyramid level
        img2d.get_array_by_coordinate(upper_left_yx=(5, 10), lower_right_yx=(20, 50), pyramid_level = 7)
    with pytest.raises(Exception) as e_info: # unknown coord pyramid level
        img2d.get_array_by_coordinate(upper_left_yx=(5, 10), lower_right_yx=(20, 50), pyramid_level_coord = 7, coordinate_unit = 'pixel')
    with pytest.raises(Exception) as e_info: # unknown coordinate unit
        img2d.get_array_by_coordinate(upper_left_yx=(5, 10), lower_right_yx=(20, 50), coordinate_unit = 'error')

    # 2D image
    assert img2d.get_array_by_coordinate() == img2d.array_dict['2']
    img0a = img2d.get_array_by_coordinate(
        upper_left_yx=None,
        lower_right_yx=None,
        size_yx=None,
        pyramid_level=2,
        as_NumPy=False)
    img0b = img2d.get_array_by_coordinate(
        upper_left_yx=(0, 0),
        lower_right_yx=(269, 319),
        size_yx=None,
        pyramid_level=2,
        as_NumPy=True)
    assert isinstance(img0a, zarr.Array)
    assert isinstance(img0b, np.ndarray)
    assert img0a.shape == (2, 1, 270, 320)
    assert (np.array(img0a) == img0b).all()

    img1a = img3d.get_array_by_coordinate(
        upper_left_yx=(22, 20),
        lower_right_yx=(44, 40),
        size_yx=None,
        coordinate_unit='pixel',
        pyramid_level=1,
        pyramid_level_coord=0,
        as_NumPy=True)
    img1b = img3d.get_array_by_coordinate(
        upper_left_yx=(11, 10),
        lower_right_yx=None,
        size_yx=(11, 10),
        coordinate_unit='pixel',
        pyramid_level=1,
        as_NumPy=True)
    img1c = img3d.get_array_by_coordinate(
        upper_left_yx=None,
        lower_right_yx=(22, 20),
        size_yx=(11, 10),
        coordinate_unit='pixel',
        pyramid_level=1,
        as_NumPy=True)
    assert isinstance(img1a, np.ndarray)
    assert isinstance(img1b, np.ndarray)
    assert isinstance(img1c, np.ndarray)
    assert img1a.shape == (2, 3, 11, 10)
    assert img1b.shape == img1a.shape
    assert img1c.shape == img1a.shape
    assert (img1b == img1a).all()
    assert (img1c == img1a).all()

    img2a = img2d.get_array_by_coordinate(
        label_name='organoids',
        upper_left_yx=(0, 0),
        lower_right_yx=(11, 10),
        size_yx=None,
        coordinate_unit='micrometer',
        pyramid_level=0,
        as_NumPy=True)
    img2b = img2d.get_array_by_coordinate(
        label_name='organoids',
        upper_left_yx=None,
        lower_right_yx=(11, 10),
        size_yx=(11, 10),
        coordinate_unit='micrometer',
        pyramid_level=0,
        as_NumPy=True)
    assert isinstance(img2a, np.ndarray)
    assert isinstance(img2b, np.ndarray)
    expected_shape = np.divide(
        [1, 11, 10], # size z, y, x in micrometer
        img2d.get_scale(0, 'organoids'))
    expected_shape = tuple([int(round(x)) for x in expected_shape])
    assert img2a.shape == expected_shape
    assert img2b.shape == img2a.shape
    assert (img1b == img1a).all()
    assert (img1c == img1a).all()

test_get_array_pair_by_coordinate(tmpdir)

Test ome_zarr.Image object get_array_pair_by_coordinate() method.

Source code in tests/test_ome_zarr.py

def test_get_array_pair_by_coordinate(tmpdir: str):
    """Test `ome_zarr.Image` object get_array_pair_by_coordinate() method."""

    # using pyramid_level corresponding to a lower resolution intensity image
    #     than any available label resolutions
    # ... copy zarr fileset
    assert tmpdir.check()
    shutil.copytree('tests/example_data/plate_ones_mip.zarr/B/03/0',
                    str(tmpdir) + '/example_img')
    assert tmpdir.join('/example_img/1').check()
    # ... remove pyramid level 2 from label organoids
    shutil.rmtree(str(tmpdir) + '/example_img/labels/organoids/2')
    zattr_file = str(tmpdir) + '/example_img/labels/organoids/.zattrs'
    with open(zattr_file) as f:
        zattr = json.load(f)
    zattr['multiscales'][0]['datasets'] = zattr['multiscales'][0]['datasets'][:2]
    with open(zattr_file, "w") as jsonfile:
        json.dump(zattr, jsonfile, indent=4)
    # ... extract array pair
    imgtmp = ome_zarr.Image(str(tmpdir) + '/example_img')
    with pytest.raises(Exception) as e_info:
        imgtmp.get_array_pair_by_coordinate(pyramid_level='2', label_name='organoids')
    # ... clean up
    shutil.rmtree(str(tmpdir) + '/example_img')

    # expected return values with multiple label_name values
    # ... copy zarr fileset
    assert tmpdir.check()
    shutil.copytree('tests/example_data/plate_ones_mip.zarr/B/03/0',
                    str(tmpdir) + '/example_img')
    assert tmpdir.join('/example_img/1').check()
    shutil.copytree(str(tmpdir) + '/example_img/labels/organoids',
                    str(tmpdir) + '/example_img/labels/cells')
    # ... initialize Image object
    img2d = ome_zarr.Image(str(tmpdir) + '/example_img')
    # ... extract array pair
    img, lab = img2d.get_array_pair_by_coordinate(label_name=['organoids', 'cells'])
    assert isinstance(img, np.ndarray)
    assert isinstance(lab, dict)
    assert list(lab.keys()) == ['organoids', 'cells']
    assert isinstance(lab['organoids'], np.ndarray)
    assert isinstance(lab['cells'], np.ndarray)
    # ... clean up
    shutil.rmtree(str(tmpdir) + '/example_img')

test_get_bounding_box_for_label_value(img2d)

Test Image.get_bounding_box_for_label_value.

Source code in tests/test_ome_zarr.py

def test_get_bounding_box_for_label_value(img2d: ome_zarr.Image):
    """Test `Image.get_bounding_box_for_label_value`."""

    # available label values
    assert img2d.get_bounding_box_for_label_value(label_value=0, label_name='organoids', label_pyramid_level='2', label_name_output='organoids', pyramid_level_output='2') == ((0, 0, 0), (1, 270, 320))
    assert img2d.get_bounding_box_for_label_value(label_value=1, label_name='organoids', label_pyramid_level='0', label_name_output='organoids', pyramid_level_output='0') == ((0, 200, 100), (1, 401, 301))
    assert img2d.get_bounding_box_for_label_value(label_value=2, label_name='organoids', label_pyramid_level='0', label_name_output='organoids', pyramid_level_output='0') == ((0, 600, 0), (1, 1001, 401))
    assert img2d.get_bounding_box_for_label_value(label_value=3, label_name='organoids', label_pyramid_level='0', label_name_output='organoids', pyramid_level_output='0') == ((0, 400, 400), (1, 1001, 1001))
    with pytest.raises(Exception) as e_info:
       img2d.get_bounding_box_for_label_value(label_value=4, label_name='organoids', label_pyramid_level='0', label_name_output='organoids', pyramid_level_output='0')

test_get_channels(img3d)

Test get_channels() method of ome_zarr.Image object.

Source code in tests/test_ome_zarr.py

def test_get_channels(img3d: ome_zarr.Image):
    """Test `get_channels()` method of `ome_zarr.Image` object."""
    assert isinstance(img3d.get_channels(), list)
    assert all([isinstance(x, dict) for x in img3d.get_channels()])
    assert all(['label' in x for x in img3d.get_channels()])

test_get_label_names(img2d)

Test get_label_names() method of ome_zarr.Image object.

Source code in tests/test_ome_zarr.py

def test_get_label_names(img2d: ome_zarr.Image):
    """Test `get_label_names()` method of `ome_zarr.Image` object."""
    assert img2d.get_label_names() == ['organoids']
    assert img2d.get_label_names() == img2d.label_names

test_get_path(img2d)

Test get_path() method of ome_zarr.Image object.

Source code in tests/test_ome_zarr.py

def test_get_path(img2d: ome_zarr.Image):
    """Test `get_path()` method of `ome_zarr.Image` object."""
    assert img2d.get_path() == 'tests/example_data/plate_ones_mip.zarr/B/03/0'
    assert img2d.get_path() == img2d.path

test_get_pyramid_levels(img2d, img3d)

Test get_pyramid_levels() method of ome_zarr.Image object.

Source code in tests/test_ome_zarr.py

def test_get_pyramid_levels(img2d: ome_zarr.Image, img3d: ome_zarr.Image):
    """Test `get_pyramid_levels()` method of `ome_zarr.Image` object."""
    assert img2d.get_pyramid_levels() == ['0', '1', '2']
    assert img2d.get_pyramid_levels(None) == ['0', '1', '2']
    assert img2d.get_pyramid_levels('organoids') == ['0', '1', '2']
    assert img3d.get_pyramid_levels() == ['0', '1', '2']

test_get_scale(img2d, img3d)

Test ome_zarr.Image object get_scale() method.

Source code in tests/test_ome_zarr.py

def test_get_scale(img2d: ome_zarr.Image, img3d: ome_zarr.Image):
    """Test `ome_zarr.Image` object get_scale() method."""

    # invalid input
    with pytest.raises(Exception) as e_info:
        img2d.get_scale()
    with pytest.raises(Exception) as e_info:
        img2d.get_scale(7)
    with pytest.raises(Exception) as e_info:
        img2d.get_scale(1, 'error')

    # 2D image with labels
    assert img2d.get_scale(0) == [1.0, 1.0, 0.1625, 0.1625]
    assert img2d.get_scale('1') == [1.0, 1.0, 0.325, 0.325]
    assert img2d.get_scale(2) == [1.0, 1.0, 0.65, 0.65]
    assert img2d.get_scale(0, 'organoids') == [1.0, 0.1625, 0.1625]
    assert img2d.get_scale('1', 'organoids') == [1.0, 0.325, 0.325]
    assert img2d.get_scale(2, 'organoids') == [1.0, 0.65, 0.65]
    assert img2d.get_scale(2, 'organoids', True) == [1.0, 0.65, 0.65]

    # 3D image
    assert img3d.get_scale(0) == [1.0, 1.0, 0.1625, 0.1625]
    assert img3d.get_scale('1') == [1.0, 1.0, 0.325, 0.325]
    assert img3d.get_scale(2) == [1.0, 1.0, 0.65, 0.65]
    assert img3d.get_scale(2, spatial_axes_only=True) == [1.0, 0.65, 0.65]

test_get_table(img2d)

Test Image.get_table().

Source code in tests/test_ome_zarr.py

def test_get_table(img2d: ome_zarr.Image):
    """Test `Image.get_table()`."""

    # invalid input
    with pytest.warns(UserWarning):
        assert img2d.get_table('error') is None

    # table as AnnData
    res1 = img2d.get_table(table_name='FOV_ROI_table',
                           as_AnnData=True)
    assert isinstance(res1, ad.AnnData)
    assert res1.shape == (4, 8)

    # table as pandas.DataFrame
    res2 = img2d.get_table(table_name='FOV_ROI_table',
                           as_AnnData=False)
    assert isinstance(res2, pd.DataFrame)
    assert res2.shape == (4, 8)

test_get_table_names(img3d)

Test get_table_names() method of ome_zarr.Image object.

Source code in tests/test_ome_zarr.py

def test_get_table_names(img3d: ome_zarr.Image):
    """Test `get_table_names()` method of `ome_zarr.Image` object."""
    assert img3d.get_table_names() == ['FOV_ROI_table']
    assert img3d.get_table_names() == img3d.table_names

test_image_str(img2d, img3d)

Test ome_zarr.Image object string representation.

Source code in tests/test_ome_zarr.py

def test_image_str(img2d: ome_zarr.Image, img3d: ome_zarr.Image):
    """Test `ome_zarr.Image` object string representation."""
    assert str(img2d) == repr(img2d)
    assert str(img3d) == repr(img3d)

test_imagelist_get_layout(imgL2)

Test ome_zarr.ImageList.get_layout.

Source code in tests/test_ome_zarr.py

def test_imagelist_get_layout(imgL2: ome_zarr.ImageList):
    """Test `ome_zarr.ImageList.get_layout`."""
    assert imgL2.get_layout().to_dict() == imgL2.layout.to_dict()
    assert isinstance(imgL2.get_layout(), pd.DataFrame)
    assert len(imgL2) == imgL2.get_layout().shape[0]

test_imagelist_get_names(imgL2)

Test ome_zarr.ImageList.get_names.

Source code in tests/test_ome_zarr.py

def test_imagelist_get_names(imgL2: ome_zarr.ImageList):
    """Test `ome_zarr.ImageList.get_names`."""
    assert imgL2.get_names() == imgL2.names
    assert len(imgL2) == len(imgL2.get_names())

test_imagelist_get_paths(imgL2)

Test ome_zarr.ImageList.get_paths.

Source code in tests/test_ome_zarr.py

def test_imagelist_get_paths(imgL2: ome_zarr.ImageList):
    """Test `ome_zarr.ImageList.get_paths`."""
    assert imgL2.get_paths() == imgL2.paths
    assert len(imgL2) == len(imgL2.get_paths())

test_imagelist_getattr(imgL)

Test ome_zarr.ImageList getting attributes of contained Image objects.

Source code in tests/test_ome_zarr.py

def test_imagelist_getattr(imgL: ome_zarr.ImageList):
    """Test `ome_zarr.ImageList` getting attributes of contained Image objects."""

    # non-existing attribute
    with pytest.raises(Exception) as e_info:
        imgL.get_nonexisting
    with pytest.raises(Exception) as e_info:
        imgL.get_nonexisting()

    # simple attributes
    assert isinstance(imgL.name, list)
    assert imgL.name == imgL.get_names()
    assert imgL.path == imgL.get_paths()

    # callable attributes
    assert imgL.get_scale('0') == [img.get_scale('0') for img in imgL.images]
    assert imgL.get_table_names() == [img.get_table_names() for img in imgL.images]

test_imagelist_getitem(imgL)

Test ome_zarr.ImageList subsetting.

Source code in tests/test_ome_zarr.py

def test_imagelist_getitem(imgL: ome_zarr.ImageList):
    """Test `ome_zarr.ImageList` subsetting."""
    assert isinstance(imgL[0], ome_zarr.Image)
    nm = imgL.names[0]
    assert isinstance(imgL[nm], ome_zarr.Image)
    assert imgL[0] == imgL[nm]
    assert str(imgL) == str(imgL[[0]])
    assert str(imgL) == str(imgL[[nm]])
    imgL2 = imgL[[0, 0]]
    assert isinstance(imgL2, ome_zarr.ImageList)
    assert len(imgL2) == 2
    assert imgL2.get_names() == [nm, nm]
    with pytest.raises(Exception) as e_info:
        imgL2[nm]
    with pytest.raises(Exception) as e_info:
        imgL2[[nm, nm]]
    imgLnolayout = imgL
    imgLnolayout.layout = None
    imgL3 = imgLnolayout[[0, 0]]
    assert len(imgL3) == 2
    assert isinstance(imgL3.layout, pd.DataFrame)

test_imagelist_plot(imgL2, tmpdir)

Test ome_zarr.ImageList.plot.

Source code in tests/test_ome_zarr.py

def test_imagelist_plot(imgL2: ome_zarr.ImageList, tmpdir: str):
    """Test `ome_zarr.ImageList.plot`."""

    imgL3 = imgL2
    imgL3.layout['row_index'] = [1, 1]
    imgL3.layout['column_index'] = [1, 1]
    with pytest.raises(Exception) as e_info:
        imgL3.plot()

    imgL2.set_layout(nrow=3)

    matplotlib.use('Agg')  # Use the 'Agg' backend, which doesn't need a display
    with warnings.catch_warnings():
        # suppress warning due to cannot show FigureCanvas
        warnings.simplefilter('ignore')

        # basic plot (no argument)
        imgL2.plot()

        # with known arguments
        imgL2.plot(fig_title = "test",
                   fig_width_inch=6,
                   fig_height_inch=4,
                   fig_dpi=100,
                   fig_style='brightfield')

        # with unknown arguments
        imgL2.plot(label_name = "organoids",
                   axis_style='frame')

    plt.savefig(tmpdir.join('output.png'))
    assert True # check if the plotting ran through

test_imagelist_set_layout(imgL2)

Test ome_zarr.ImageList.set_layout.

Source code in tests/test_ome_zarr.py

def test_imagelist_set_layout(imgL2: ome_zarr.ImageList):
    """Test `ome_zarr.ImageList.set_layout`."""
    df = copy.deepcopy(imgL2.get_layout())
    assert isinstance(df, pd.DataFrame)
    assert df.columns.to_list() == ['row_index', 'column_index']
    with pytest.raises(Exception) as e_info:
        imgL2.set_layout(df.iloc[[0]])
    df['row_index'] = [4, 5]
    imgL2.set_layout(layout=df)
    assert imgL2.get_layout().to_dict() == df.to_dict()
    imgL2.set_layout(nrow=7)
    assert imgL2.nrow == 7
    imgL2.set_layout(ncol=4, by_row=True)
    assert imgL2.ncol == 4
    imgL2.set_layout(nrow = 2, reset_names=True)
    assert imgL2.get_names() == ['1_1', '2_1']
    with pytest.warns(UserWarning):
        imgL2.set_layout(layout='grid', nrow=2)
    assert isinstance(imgL2.get_layout(), pd.DataFrame)
    with pytest.raises(Exception) as e_info:
        imgL2.set_layout(layout='error')

test_imagelist_str(imgL)

Test ome_zarr.ImageList object string representation.

Source code in tests/test_ome_zarr.py

def test_imagelist_str(imgL: ome_zarr.ImageList):
    """Test `ome_zarr.ImageList` object string representation."""
    assert str(imgL) == repr(imgL)
    assert str(imgL).startswith('ImageList of 1 image')
    imgLmod = imgL
    imgLmod.names = [''.join(imgL.names * 50)]
    imgLmod.paths = ['/'.join(imgL.paths * 5)]
    assert str(imgLmod) == repr(imgLmod)

test_import_plate(tmpdir)

Test import_plate function.

Source code in tests/test_ome_zarr.py

def test_import_plate(tmpdir: str):
    """Test `import_plate` function."""
    with pytest.raises(Exception) as e_info:
        ome_zarr.import_plate()
    with pytest.raises(Exception) as e_info:
        ome_zarr.import_plate('tests/example_data')
    imgL = ome_zarr.import_plate('tests/example_data/plate_ones_mip.zarr')
    assert isinstance(imgL, ome_zarr.ImageList)
    assert len(imgL) == 1
    assert imgL.names == ['B03']
    assert imgL.paths == ['tests/example_data/plate_ones_mip.zarr/B/03/0']
    assert imgL.nrow == 2
    assert imgL.ncol == 3
    assert imgL.layout.to_dict() == {'row_index': {0: 2}, 'column_index': {0: 3}}

    shutil.copytree('tests/example_data/plate_ones_mip.zarr',
                    str(tmpdir) + '/example_img')
    assert tmpdir.join('/example_img/.zattrs').check()
    shutil.move(str(tmpdir) + '/example_img/B/03',
                str(tmpdir) + '/example_img/B/10')
    with pytest.raises(Exception) as e_info:
        with pytest.warns(UserWarning):
            imgL2 = ome_zarr.import_plate(str(tmpdir) + '/example_img')
    # add B10 to omero attributes
    zattr_file = str(tmpdir) + '/example_img/.zattrs'
    with open(zattr_file) as f:
       zattr = json.load(f)
    zattr['plate']['columns'].append({'name': '10'})
    zattr['plate']['wells'].append({'columnIndex': 1, 'path': 'B/10', 'rowIndex': 0})
    with open(zattr_file, "w") as jsonfile:
        json.dump(zattr, jsonfile, indent=4)
    with pytest.warns(UserWarning):
        imgL2 = ome_zarr.import_plate(str(tmpdir) + '/example_img')
    assert imgL2.nrow == 8
    assert imgL2.ncol == 12

    shutil.copytree('tests/example_data/plate_ones_mip.zarr',
                    str(tmpdir) + '/example_img_multi')
    assert tmpdir.join('/example_img_multi/.zattrs').check()
    shutil.copytree(str(tmpdir) + '/example_img_multi/B/03',
                    str(tmpdir) + '/example_img_multi/C/02')
    shutil.copytree(str(tmpdir) + '/example_img_multi/B/03',
                    str(tmpdir) + '/example_img_multi/G/06')
    imgL3 = ome_zarr.import_plate(str(tmpdir) + '/example_img_multi')
    assert len(imgL3) == 1
    assert imgL3.names == ['B03']
    # add additional images to metadata
    zattr_file = str(tmpdir) + '/example_img_multi/.zattrs'
    with open(zattr_file) as f:
       zattr = json.load(f)
    zattr['plate']['columns'].append({'name': '02'})
    zattr['plate']['rows'].append({'name': 'C'})
    zattr['plate']['wells'].append({'columnIndex': 1, 'path': 'C/02', 'rowIndex': 1})
    zattr['plate']['columns'].append({'name': '06'})
    zattr['plate']['rows'].append({'name': 'G'})
    zattr['plate']['wells'].append({'columnIndex': 2, 'path': 'G/06', 'rowIndex': 2})
    with open(zattr_file, "w") as jsonfile:
        json.dump(zattr, jsonfile, indent=4)
    imgL3 = ome_zarr.import_plate(str(tmpdir) + '/example_img_multi')
    assert imgL3.nrow == 8
    assert imgL3.ncol == 12
    assert imgL3.layout.row_index.tolist() == [2, 3, 7]
    assert imgL3.layout.column_index.tolist() == [3, 2, 6]
    assert imgL3['B03'].get_path() == str(tmpdir) + '/example_img_multi/B/03/0'
    assert imgL3['C02'].get_path() == str(tmpdir) + '/example_img_multi/C/02/0'
    assert imgL3['G06'].get_path() == str(tmpdir) + '/example_img_multi/G/06/0'
    assert imgL3.paths == [str(tmpdir) + '/example_img_multi/B/03/0', str(tmpdir) + '/example_img_multi/C/02/0', str(tmpdir) + '/example_img_multi/G/06/0']
    assert imgL3.names == ['B03', 'C02', 'G06']

test_load_axes_unit(img2d)

Test Image._load_axes_unit.

Source code in tests/test_ome_zarr.py

def test_load_axes_unit(img2d: ome_zarr.Image):
    """Test `Image._load_axes_unit`."""

    # missing unit
    multiscale_dict = copy.deepcopy(img2d.multiscales_image)
    del multiscale_dict['axes'][1]['unit']
    del multiscale_dict['axes'][2]['unit']
    del multiscale_dict['axes'][3]['unit']
    assert img2d._load_axes_unit(multiscale_dict) == 'pixel'

    # unsupported unit
    multiscale_dict = copy.deepcopy(img2d.multiscales_image)
    multiscale_dict['axes'][2]['unit'] = 'parsec'
    with pytest.raises(Exception) as e_info:
        img2d._load_axes_unit(multiscale_dict)

    # test loading
    # ... inensity image
    out_axes_unit_image = img2d._load_axes_unit(img2d.multiscales_image)
    assert out_axes_unit_image == 'micrometer'
    # ... labels
    out_axes_unit_labels = {x: img2d._load_axes_unit(img2d.multiscales_labels[x]) for x in img2d.label_names}
    assert 'organoids' in out_axes_unit_labels
    assert out_axes_unit_labels['organoids'] == 'micrometer'

test_load_channel_info(img3d, img2d)

Test Image._load_channel_info.

Source code in tests/test_ome_zarr.py

def test_load_channel_info(img3d: ome_zarr.Image, img2d: ome_zarr.Image):
    """Test `Image._load_channel_info`."""

    # input with missing axes
    with pytest.raises(Exception) as e_info:
        img3d._load_channel_info({})

    # example input
    assert img2d._load_channel_info(img2d.multiscales_image) == 'czyx'
    assert img3d._load_channel_info(img3d.multiscales_image) == 'czyx'

    # synthetic input
    assert img2d._load_channel_info(
        {'axes': [{'name': 'day', 'type': 'time'},
                  {'name': 'c', 'type': 'channel'},
                  {'name': 'y', 'type': 'space'},
                  {'name': 'x', 'type': 'space'}]}) == 'tcyx'
    assert img2d._load_channel_info(
        {'axes': [{'name': 'c', 'type': 'channel'},
                  {'name': 'y', 'type': 'space'},
                  {'name': 'x', 'type': 'space'}]}) == 'cyx'
    assert img2d._load_channel_info(
        {'axes': [{'name': 'y', 'type': 'space'},
                  {'name': 'x', 'type': 'space'}]}) == 'yx'

test_load_multiscale_info(img2d, tmpdir)

Test Image._load_multiscale_info.

Source code in tests/test_ome_zarr.py

def test_load_multiscale_info(img2d: ome_zarr.Image, tmpdir: str):
    """Test `Image._load_multiscale_info`."""

    # missing multiscales attributes
    # ... copy zarr fileset
    assert tmpdir.check()
    shutil.copytree('tests/example_data/plate_ones_mip.zarr/B/03/0',
                    str(tmpdir) + '/example_img')
    assert tmpdir.join('/example_img/.zattrs').check()
    # ... copy original .zattrs
    zattr_file = str(tmpdir) + '/example_img/.zattrs'
    shutil.copyfile(zattr_file, zattr_file + '.orig')
    # ... remove multiscales attributes from copy
    with open(zattr_file) as f:
       zattr = json.load(f)
    del zattr['multiscales']
    with open(zattr_file, "w") as jsonfile:
        json.dump(zattr, jsonfile, indent=4)
    # ... test loading
    with pytest.raises(Exception) as e_info:
        ome_zarr.Image(str(tmpdir) + '/example_img')
    # ... restore original .zattrs
    shutil.move(zattr_file + '.orig', zattr_file)

    # missing label multiscales attrs
    assert tmpdir.join('/example_img/labels/organoids/.zattrs').check()
    # ... copy original .zattrs
    zattr_file = str(tmpdir) + '/example_img/labels/organoids/.zattrs'
    shutil.copyfile(zattr_file, zattr_file + '.orig')
    # ... remove multiscales attributes from copy
    with open(zattr_file) as f:
       zattr = json.load(f)
    del zattr['multiscales']
    with open(zattr_file, "w") as jsonfile:
        json.dump(zattr, jsonfile, indent=4)
    # ... test loading
    with pytest.raises(Exception) as e_info:
        ome_zarr.Image(str(tmpdir) + '/example_img')
    # ... restore original .zattrs
    shutil.move(zattr_file + '.orig', zattr_file)

    # multiple multiscales dictionaries
    assert tmpdir.join('/example_img/.zattrs').check()
    # ... copy original .zattrs
    zattr_file = str(tmpdir) + '/example_img/.zattrs'
    shutil.copyfile(zattr_file, zattr_file + '.orig')
    # ... duplicate multiscales attributes in copy
    with open(zattr_file) as f:
       zattr = json.load(f)
    zattr['multiscales'].append(zattr['multiscales'][0])
    with open(zattr_file, "w") as jsonfile:
        json.dump(zattr, jsonfile, indent=4)
    # ... test loading
    with pytest.warns(UserWarning):
        ome_zarr.Image(str(tmpdir) + '/example_img')
    # ... restore original .zattrs
    shutil.move(zattr_file + '.orig', zattr_file)

    # missing axes in multiscales attrs
    assert tmpdir.join('/example_img/.zattrs').check()
    # ... copy original .zattrs
    zattr_file = str(tmpdir) + '/example_img/.zattrs'
    shutil.copyfile(zattr_file, zattr_file + '.orig')
    # ... remove axes multiscales attributes in copy
    with open(zattr_file) as f:
       zattr = json.load(f)
    del zattr['multiscales'][0]['axes']
    with open(zattr_file, "w") as jsonfile:
        json.dump(zattr, jsonfile, indent=4)
    # ... test loading
    with pytest.raises(Exception) as e_info:
        ome_zarr.Image(str(tmpdir) + '/example_img')
    # ... restore original .zattrs
    shutil.move(zattr_file + '.orig', zattr_file)

    # test loading
    # ... intensity image
    out_multiscales_image = img2d._load_multiscale_info(img2d.zarr_group, False)
    assert isinstance(out_multiscales_image, dict)
    assert 'axes' in out_multiscales_image
    assert 'datasets' in out_multiscales_image
    assert isinstance(out_multiscales_image['axes'], list)
    assert isinstance(out_multiscales_image['datasets'], list)
    # ... labels
    out_multiscales_labels = {x: img2d._load_multiscale_info(img2d.zarr_group.labels[x], False) for x in img2d.label_names}
    assert 'organoids' in out_multiscales_labels
    assert isinstance(out_multiscales_labels['organoids'], dict)
    assert 'axes' in out_multiscales_labels['organoids']
    assert 'datasets' in out_multiscales_labels['organoids']
    assert isinstance(out_multiscales_labels['organoids']['axes'], list)
    assert isinstance(out_multiscales_labels['organoids']['datasets'], list)

test_plot(img2d, tmpdir)

Test Image.plot().

Source code in tests/test_ome_zarr.py

def test_plot(img2d: ome_zarr.Image, tmpdir: str):
    """Test `Image.plot()`."""

    matplotlib.use('Agg')  # Use the 'Agg' backend, which doesn't need a display
    with warnings.catch_warnings():
        # suppress warning due to cannot show FigureCanvas
        warnings.simplefilter('ignore')

        # using channels_labels
        img2d.plot(label_name=None,
                   pyramid_level=None,
                   pyramid_level_coord=None,
                   channels_labels=['some-label-1'],
                   channel_colors=['white'],
                   channel_ranges=[[0.01, 0.99]],
                   z_projection_method='maximum',
                   scalebar_micrometer=50,
                   show_scalebar_label=True)

        # unknown channel label
        with pytest.raises(Exception) as e_info:
            img2d.plot(channels_labels=['error'],
                       pyramid_level_coord=2)

        # both channels and channels_labels given
        with pytest.warns(UserWarning):
            img2d.plot(channels=[0],
                       channels_labels=['some-label-2'],
                       scalebar_micrometer=50,
                       show_scalebar_label=False)

        # automatically extract channel colors and ranges
        img2d.plot(channels=[0])

        # using label_name
        img2d.plot(label_name='organoids',
                   channels=[0],
                   channel_colors=['white'],
                   channel_ranges=[[0.01, 0.99]])
        img2d.plot(label_name=['non-existent', 'also-non-existent', 'organoids'],
                   channels=[0],
                   channel_colors=['white'],
                   channel_ranges=[[0.01, 0.99]])
        img2d.plot(label_name=['non-existent', 'also-non-existent'],
                   channels=[0],
                   channel_colors=['white'],
                   channel_ranges=[[0.01, 0.99]])

        # automatically extract coordinates for label_value
        with pytest.warns(UserWarning):
            img2d.plot(upper_left_yx=(0, 0),
                       lower_right_yx=(100, 100),label_name='organoids',
                       label_value=3,
                       extend_pixels=8)

        # ... restrict plotting to label_value
        img2d.plot(label_name='organoids',
                   label_value=3,
                   restrict_to_label_values=[3])

        # ... restrict plotting to non-existent label_value
        img2d.plot(label_name='organoids',
                   label_value=3,
                   restrict_to_label_values=99)

        # ... non-existent label_value
        with pytest.raises(Exception) as e_info:
            img2d.plot(label_name='organoids',
                       label_value=99)

        # using label_name without matching pyrmaid level
        # ... copy zarr fileset
        assert tmpdir.check()
        shutil.copytree('tests/example_data/plate_ones_mip.zarr/B/03/0',
                        str(tmpdir) + '/example_img')
        assert tmpdir.join('/example_img/1').check()
        # ... remove pyramid levels 1 and 2 from image
        shutil.rmtree(str(tmpdir) + '/example_img/1')
        shutil.rmtree(str(tmpdir) + '/example_img/2')
        zattr_file = str(tmpdir) + '/example_img/.zattrs'
        with open(zattr_file) as f:
            zattr = json.load(f)
        zattr['multiscales'][0]['datasets'] = [zattr['multiscales'][0]['datasets'][0]]
        with open(zattr_file, "w") as jsonfile:
            json.dump(zattr, jsonfile, indent=4)
        # ... remove pyramid levels 0 and 1 from label organoids
        shutil.rmtree(str(tmpdir) + '/example_img/labels/organoids/0')
        shutil.rmtree(str(tmpdir) + '/example_img/labels/organoids/1')
        zattr_file = str(tmpdir) + '/example_img/labels/organoids/.zattrs'
        with open(zattr_file) as f:
            zattr = json.load(f)
        zattr['multiscales'][0]['datasets'] = [zattr['multiscales'][0]['datasets'][2]]
        with open(zattr_file, "w") as jsonfile:
            json.dump(zattr, jsonfile, indent=4)
        # ... plot
        imgtmp = ome_zarr.Image(str(tmpdir) + '/example_img')
        imgtmp.plot(label_name='organoids')
        # ... clean up
        shutil.rmtree(str(tmpdir) + '/example_img')
        ### TODO: problematic case where pyramid_level_coord is not None
        ###       and pyramid_level is not parallel in image and label
        ###       what does pyramid_level_coord refer to?
        ###       solution: remove pyramid_level_coord argument?
        ###       not needed: can use coordinate_unit="micrometer"

    plt.savefig(tmpdir.join('output.png'))
    assert True # check if the plotting ran through

test_tree(img2d)

Test Image.tree().

Source code in tests/test_ome_zarr.py

def test_tree(img2d: ome_zarr.Image):
    """Test `Image.tree()`."""

    res1 = img2d.tree()
    assert print(res1) == None
    res2 = img2d.tree(expand=True, level=2)
    assert isinstance(res2, zarr.util.TreeViewer)

plotting

npa3d()

A 3D numpy.array with shape (3,4,5)

Source code in tests/test_plotting.py

@pytest.fixture
def npa3d() -> np.ndarray:
    """A 3D `numpy.array` with shape (3,4,5)"""
    np.random.seed(42)
    return np.random.randint(0, 16, size=(3, 4, 5))

npa4d()

A 4D numpy.array with shape (2,3,4,5)

Source code in tests/test_plotting.py

@pytest.fixture
def npa4d() -> np.ndarray:
    """A 4D `numpy.array` with shape (2,3,4,5)"""
    np.random.seed(42)
    return np.random.randint(0, 2**16, size=(2, 3, 4, 5))

test_convert_to_rgb(npa3d)

Test convert_to_rgb.

Source code in tests/test_plotting.py

def test_convert_to_rgb(npa3d: np.ndarray):
    """Test convert_to_rgb."""
    rng = np.quantile(npa3d[1], [0.01, 0.5])
    rgb = convert_to_rgb(im=npa3d[[0,1]],
                         channel_colors=['yellow', 'red'],
                         channel_ranges=[[0.01, 0.5], rng])
    assert isinstance(rgb, np.ndarray)
    assert rgb.shape == (npa3d.shape[1], npa3d.shape[2], 3)
    assert rgb.dtype == np.uint8
    assert np.max(rgb) == 255
    da = dask.array.from_array(npa3d)
    rgb = convert_to_rgb(im=da[[0,1]],
                         channel_colors=['yellow', 'red'],
                         channel_ranges=[[0.01, 0.5], rng])
    assert isinstance(rgb, np.ndarray)
    assert rgb.shape == (npa3d.shape[1], npa3d.shape[2], 3)
    assert rgb.dtype == np.uint8
    assert np.max(rgb) == 255

test_get_shuffled_cmap()

Test get_shuffled_cmap.

Source code in tests/test_plotting.py

def test_get_shuffled_cmap():
    """Test get_shuffled_cmap."""
    cm = get_shuffled_cmap()
    assert isinstance(cm, mcolors.ListedColormap)

test_pad_image(npa3d)

Test pad_image.

Source code in tests/test_plotting.py

def test_pad_image(npa3d: np.ndarray):
    """Test pad_image."""
    pad = (0, 20, 30)
    out = tuple(pad[i] + npa3d.shape[i] for i in range(3))
    impad = pad_image(im = npa3d, output_shape=out)
    assert impad.shape == out
    assert (impad[:, slice(10, 10 + npa3d.shape[1]), slice(15, 15 + npa3d.shape[2])] == npa3d).all()

test_plot_image(npa4d, npa3d, tmpdir)

Test plot_image.

Source code in tests/test_plotting.py

def test_plot_image(npa4d: np.ndarray, npa3d: np.ndarray, tmpdir: str):
    """Test plot_image."""
    with pytest.raises(Exception) as e_info:
        plot_image(im=npa4d, msk=None,
                   channels=[1],
                   channel_colors=['white'],
                   channel_ranges=[[0.01, 0.99]],
                   title='test', call_show=False,
                   scalebar_pixel=100,
                   scalebar_position='error')

    with pytest.raises(Exception) as e_info:
        plot_image(im=npa4d, msk=None,
                   channels=[1],
                   channel_colors=['white'],
                   channel_ranges=[[0.01, 0.99]],
                   title='test', call_show=False,
                   axis_style='error')

    matplotlib.use('Agg')  # Use the 'Agg' backend, which doesn't need a display
    with warnings.catch_warnings():
        warnings.simplefilter('ignore') # suppress warning due to cannot show FigureCanvas 
        # scalebar_position
        for pos in ['topleft', 'bottomleft', 'topright', 'bottomright']:
            plot_image(im=npa4d, msk=None,
                    channels=[1],
                    channel_colors=['white'],
                    channel_ranges=[[0.01, 0.99]],
                    title='test', title_fontsize='xx-large', call_show=False,
                    scalebar_pixel=100, scalebar_fontsize=10,
                    scalebar_position=pos,
                    scalebar_label='test')
        # axis_style and image_transform
        for st in ['none', 'pixel', 'frame', 'micrometer']:
            plot_image(im=npa4d, msk=None,
                       channels=[1],
                       channel_colors=['white'],
                       channel_ranges=[[0.01, 0.99]],
                       title='test', call_show=False,
                       image_transform=np.log1p,
                       axis_style=st,
                       spacing_yx=[0.325, 0.325])
        # image with masks
        plot_image(im=npa4d, msk=npa3d,
                   channels=[1],
                   channel_colors=['white'],
                   channel_ranges=[[0.01, 0.99]],
                   title='test', call_show=True)
        plot_image(im=npa4d, msk=npa3d,
                   channels=[1],
                   channel_colors=['white'],
                   channel_ranges=[[0.01, 0.99]],
                   show_label_values=True,
                   label_text_colour='red', label_fontsize=12,
                   title='test', call_show=True)
        # brightfield image
        plot_image(im=npa4d[slice(0,1)],
                   call_show=True,
                   fig_style='brightfield')
        # 2D image
        plot_image(im=npa4d[0, 0],
                   call_show=True)
    plt.savefig(tmpdir.join('output.png'))
    assert True # check if the plotting ran through

test_zproject(npa3d, npa4d)

Test zproject.

Source code in tests/test_plotting.py

def test_zproject(npa3d: np.ndarray, npa4d: np.ndarray):
    """Test zproject."""
    with pytest.raises(Exception) as e_info:
        zproject(im=npa3d, axis=1, method='error')

    r3d0max = zproject(im=npa3d, axis=0, method='maximum',
                       keepdims=True, img_bit=16)
    r3d0min = zproject(im=npa3d, axis=0, method='minimum',
                    keepdims=True, img_bit=16)
    r3d0sum = zproject(im=npa3d, axis=0, method='sum',
                       keepdims=True, img_bit=16)
    r3d0avg = zproject(im=npa3d, axis=0, method='average',
                       keepdims=True, img_bit=16)
    r4d1sum_noclip = zproject(im=npa4d, axis=1, method='sum',
                              keepdims=True, img_bit=32)
    r4d1avg_reddim = zproject(im=npa4d, axis=1, method='average',
                              keepdims=False, img_bit=16)
    assert isinstance(r3d0max, np.ndarray)
    assert r3d0max.shape == (1,4,5)
    assert r3d0min.shape == r3d0max.shape
    assert r3d0sum.shape == r3d0max.shape
    assert r3d0avg.shape == r3d0max.shape
    assert r4d1sum_noclip.shape == (2,1,4,5)
    assert r4d1avg_reddim.shape == (2,4,5)
    assert (r3d0max == np.max(npa3d, axis=0, keepdims=True)).all()
    assert (r3d0min == np.min(npa3d, axis=0, keepdims=True)).all()
    assert (r3d0sum == np.clip(np.sum(npa3d, axis=0, keepdims=True), 0, 2**16)).all()
    assert (r3d0avg == np.mean(npa3d, axis=0, keepdims=True)).all()
    assert (r4d1sum_noclip == np.sum(npa4d, axis=1, keepdims=True)).all()
    assert (r4d1avg_reddim == np.mean(npa4d, axis=1, keepdims=False)).all()

hcs_wrappers

plate_2d()

A hcs_wrappers.FractalZarr object representing a 2D ome-zarr fileset

Source code in tests/test_hcs_wrappers.py

@pytest.fixture
def plate_2d():
    """A `hcs_wrappers.FractalZarr` object representing a 2D ome-zarr fileset"""
    return hcs_wrappers.FractalZarr('tests/example_data/plate_ones_mip.zarr', name="test")

plate_3d()

A hcs_wrappers.FractalZarr object representing a 3D ome-zarr fileset

Source code in tests/test_hcs_wrappers.py

@pytest.fixture
def plate_3d():
    """A `hcs_wrappers.FractalZarr` object representing a 3D ome-zarr fileset"""
    return hcs_wrappers.FractalZarr('tests/example_data/plate_ones.zarr')

plate_set1()

A hcs_wrappers.FractalZarrSet object representing a two ome-zarr filesets

Source code in tests/test_hcs_wrappers.py

@pytest.fixture
def plate_set1():
    """A `hcs_wrappers.FractalZarrSet` object representing a two ome-zarr filesets"""
    return hcs_wrappers.FractalZarrSet('tests/example_data')

plate_set2()

A hcs_wrappers.FractalZarrSet object representing a two ome-zarr filesets

Source code in tests/test_hcs_wrappers.py

@pytest.fixture
def plate_set2():
    """A `hcs_wrappers.FractalZarrSet` object representing a two ome-zarr filesets"""
    return hcs_wrappers.FractalZarrSet('tests/example_data', name="test")

test_calc_average_FOV(tmpdir, plate_3d)

Test FractalZarr.calc_average_FOV().

Source code in tests/test_hcs_wrappers.py

def test_calc_average_FOV(tmpdir: str, plate_3d: hcs_wrappers.FractalZarr):
    """Test `FractalZarr.calc_average_FOV().`"""
    # test exceptions
    # ... copy zarr fileset
    assert tmpdir.check()
    shutil.copytree('tests/example_data', str(tmpdir) + '/example_data')
    assert tmpdir.join('/example_data/plate_ones.zarr/B/03/0/tables/FOV_ROI_table').check()
    # ... remove tables
    shutil.rmtree(str(tmpdir) + '/example_data/plate_ones.zarr/B/03/0/tables')
    # ... test calculation
    plate_tmp = hcs_wrappers.FractalZarr(str(tmpdir) + '/example_data/plate_ones.zarr')
    with pytest.raises(Exception) as e_info:
        plate_tmp.calc_average_FOV()

    # test expected results
    avg0 = plate_3d.calc_average_FOV(pyramid_level=0)
    avg1 = plate_3d.calc_average_FOV(pyramid_level=1)
    avg2 = plate_3d.calc_average_FOV(pyramid_level=2)

    assert isinstance(avg0, np.ndarray)
    assert isinstance(avg1, np.ndarray)
    assert isinstance(avg2, np.ndarray)

    assert avg0.shape == (3, 540, 640)
    assert avg1.shape == (3, 270, 320)
    assert avg2.shape == (3, 135, 160)

test_constructor_2d(plate_2d)

Test the FractalZarr constructor (2D).

Source code in tests/test_hcs_wrappers.py

def test_constructor_2d(plate_2d: hcs_wrappers.FractalZarr):
    """Test the `FractalZarr` constructor (2D)."""
    assert isinstance(plate_2d, hcs_wrappers.FractalZarr)
    assert plate_2d.name == 'test'
    assert isinstance(plate_2d._FractalZarr__top, zarr.Group)
    assert plate_2d.columns == [{'name': '03'}]
    assert plate_2d.rows == [{'name': 'B'}]
    assert len(plate_2d.wells) == 1
    assert len(plate_2d.channels) == 2
    assert isinstance(plate_2d.channels[0], dict)
    assert isinstance(plate_2d.multiscales_images, dict)
    assert 'datasets' in plate_2d.multiscales_images['0']
    assert len(plate_2d.multiscales_images['0']['datasets']) == 3
    assert plate_2d.level_paths_images['0'] == list(range(3))
    assert plate_2d.level_zyx_spacing_images['0'] == [[1.0, 0.1625, 0.1625], [1.0, 0.325, 0.325], [1.0, 0.65, 0.65]]
    assert list(plate_2d.level_zyx_scalefactor['0']) == [1., 2., 2.]
    assert plate_2d.label_names == ['organoids']
    assert plate_2d.table_names == ['FOV_ROI_table']

test_constructor_3d(plate_3d)

Test the FractalZarr constructor (3D).

Source code in tests/test_hcs_wrappers.py

def test_constructor_3d(plate_3d: hcs_wrappers.FractalZarr):
    """Test the `FractalZarr` constructor (3D)."""
    # exceptions
    with pytest.raises(Exception) as e_info:
        hcs_wrappers.FractalZarr('does-not-exist')
    with pytest.raises(Exception) as e_info:
        hcs_wrappers.FractalZarr('tests/example_data/plate_ones_mip.zarr/B')

    # expected values
    assert isinstance(plate_3d, hcs_wrappers.FractalZarr)
    assert plate_3d.name == 'plate_ones.zarr'
    assert isinstance(plate_3d._FractalZarr__top, zarr.Group)
    assert plate_3d.columns == [{'name': '03'}]
    assert plate_3d.rows == [{'name': 'B'}]
    assert len(plate_3d.wells) == 1
    assert len(plate_3d.channels) == 2
    assert isinstance(plate_3d.channels[0], dict)
    assert isinstance(plate_3d.multiscales_images, dict)
    assert 'datasets' in plate_3d.multiscales_images['0']
    assert len(plate_3d.multiscales_images['0']['datasets']) == 3
    assert plate_3d.level_paths_images['0'] == list(range(3))
    assert plate_3d.level_zyx_spacing_images['0'] == [[1.0, 0.1625, 0.1625], [1.0, 0.325, 0.325], [1.0, 0.65, 0.65]]
    assert list(plate_3d.level_zyx_scalefactor['0']) == [1., 2., 2.]
    assert plate_3d.label_names == []
    assert plate_3d.table_names == ['FOV_ROI_table']

test_constructor_set(plate_set1, plate_set2, tmpdir)

Test FractalZarrSet object constructor.

Source code in tests/test_hcs_wrappers.py

def test_constructor_set(plate_set1: hcs_wrappers.FractalZarrSet,
                         plate_set2: hcs_wrappers.FractalZarrSet,
                         tmpdir: str):
    """Test `FractalZarrSet` object constructor."""
    # exceptions
    with pytest.raises(Exception) as e_info:
        hcs_wrappers.FractalZarrSet('error')

    with pytest.raises(Exception) as e_info:
        hcs_wrappers.FractalZarrSet(tmpdir)

    # expected values    
    assert isinstance(plate_set1, hcs_wrappers.FractalZarrSet)
    assert plate_set1.path == 'tests/example_data'
    assert plate_set1.name == 'example_data'
    assert plate_set2.name == 'test'
    assert plate_set1.zarr_mip_idx == 0
    assert plate_set1.zarr_3d_idx == 1

test_coordinate_conversions(plate_3d, plate_2d)

Test FractalZarr.convert_* coordinate conversions.

Source code in tests/test_hcs_wrappers.py

def test_coordinate_conversions(plate_3d: hcs_wrappers.FractalZarr, plate_2d: hcs_wrappers.FractalZarr):
    """Test `FractalZarr.convert_*` coordinate conversions."""
    # test exceptions
    with pytest.raises(Exception) as e_info:
        plate_3d.convert_micrometer_to_pixel('error')
    with pytest.raises(Exception) as e_info:
        plate_3d.convert_pixel_to_micrometer('error')
    with pytest.raises(Exception) as e_info:
        plate_3d.convert_pixel_to_pixel('error', 0, 0)
    with pytest.raises(Exception) as e_info:
        plate_2d.convert_micrometer_to_pixel(zyx=(1,2,3), pyramid_level=0,
                                             pyramid_ref=('label', 'does-not-exist'))

    # test expected results
    # ... image coordinates
    zyx_um_orig = (30, 40, 50)
    zyx_px_0 = plate_3d.convert_micrometer_to_pixel(zyx=zyx_um_orig, pyramid_level=0,
                                                    pyramid_ref=('image', '0'))
    zyx_px_1 = plate_3d.convert_micrometer_to_pixel(zyx=zyx_um_orig, pyramid_level=1)
    zyx_px_2 = plate_3d.convert_micrometer_to_pixel(zyx=zyx_um_orig, pyramid_level=2)
    zyx_um_from1 = plate_3d.convert_pixel_to_micrometer(zyx=zyx_px_1, pyramid_level=1)
    zyx_um_from2 = plate_3d.convert_pixel_to_micrometer(zyx=zyx_px_2, pyramid_level=2)
    zyx_px_0_from1 = plate_3d.convert_pixel_to_pixel(zyx=zyx_px_1, pyramid_level_from=1, pyramid_level_to=0)
    zyx_px_2_from1 = plate_3d.convert_pixel_to_pixel(zyx=zyx_px_1, pyramid_level_from=1, pyramid_level_to=2)
    assert isinstance(zyx_px_1, tuple)
    assert all([isinstance(v, np.int_) for v in zyx_px_1])
    assert len(zyx_px_1) == 3
    assert zyx_px_1 == (30, 123, 154)
    assert zyx_um_from1 == zyx_um_orig
    assert zyx_um_from2 == zyx_um_orig
    assert zyx_px_0_from1 == zyx_px_0
    assert zyx_px_2_from1 == zyx_px_2

    # ... label coordinates
    ref = ('label', 'organoids')
    zyx_px_0 = plate_2d.convert_micrometer_to_pixel(zyx=zyx_um_orig, pyramid_level=0,
                                                    pyramid_ref=ref)
    zyx_px_1 = plate_2d.convert_micrometer_to_pixel(zyx=zyx_um_orig, pyramid_level=1, pyramid_ref=ref)
    zyx_px_2 = plate_2d.convert_micrometer_to_pixel(zyx=zyx_um_orig, pyramid_level=2, pyramid_ref=ref)
    zyx_um_from1 = plate_2d.convert_pixel_to_micrometer(zyx=zyx_px_1, pyramid_level=1, pyramid_ref=ref)
    zyx_um_from2 = plate_2d.convert_pixel_to_micrometer(zyx=zyx_px_2, pyramid_level=2, pyramid_ref=ref)
    zyx_px_0_from1 = plate_2d.convert_pixel_to_pixel(zyx=zyx_px_1, pyramid_level_from=1, pyramid_level_to=0, 
                                                     pyramid_ref_from=ref, pyramid_ref_to=ref)
    zyx_px_2_from1 = plate_2d.convert_pixel_to_pixel(zyx=zyx_px_1, pyramid_level_from=1, pyramid_level_to=2, 
                                                     pyramid_ref_from=ref, pyramid_ref_to=ref)
    assert isinstance(zyx_px_1, tuple)
    assert all([isinstance(v, np.int_) for v in zyx_px_1])
    assert len(zyx_px_1) == 3
    assert zyx_px_1 == (30, 123, 154)
    assert zyx_um_from1 == zyx_um_orig
    assert zyx_um_from2 == zyx_um_orig
    assert zyx_px_0_from1 == zyx_px_0
    assert zyx_px_2_from1 == zyx_px_2

test_digest_include_wells_argument(plate_3d)

Test FractalZarr._digest_include_wells_argument.

Source code in tests/test_hcs_wrappers.py

def test_digest_include_wells_argument(plate_3d: hcs_wrappers.FractalZarr):
    """Test `FractalZarr._digest_include_wells_argument`."""
    assert plate_3d._digest_include_wells_argument([]) == ['B/03']
    assert plate_3d._digest_include_wells_argument(['B03']) == ['B/03']
    assert plate_3d._digest_include_wells_argument('B03') == ['B/03']

test_digest_pyramid_level_argument(plate_3d, plate_2d)

Test FractalZarr._digest_pyramid_level_argument.

Source code in tests/test_hcs_wrappers.py

def test_digest_pyramid_level_argument(plate_3d: hcs_wrappers.FractalZarr, plate_2d: hcs_wrappers.FractalZarr):
    """Test `FractalZarr._digest_pyramid_level_argument`."""
    assert plate_3d._digest_pyramid_level_argument(None) == 2
    assert plate_3d._digest_pyramid_level_argument(1) == 1
    assert plate_3d._digest_pyramid_level_argument(1, ('image', '0')) == 1
    assert plate_2d._digest_pyramid_level_argument(1, ('label', 'organoids')) == 1
    assert plate_2d._digest_pyramid_level_argument(None, ('label', 'organoids')) == 2

test_digest_well_argument(plate_3d)

Test FractalZarr._digest_well_argument.

Source code in tests/test_hcs_wrappers.py

def test_digest_well_argument(plate_3d: hcs_wrappers.FractalZarr):
    """Test `FractalZarr._digest_well_argument`."""
    assert plate_3d._digest_well_argument(None) == 'B/03'
    assert plate_3d._digest_well_argument('B03') == 'B/03'
    assert plate_3d._digest_well_argument('B03', as_path=False) == 'B03'

test_get_channels(plate_2d, plate_3d)

Test FractalZarr.get_channels().

Source code in tests/test_hcs_wrappers.py

def test_get_channels(plate_2d: hcs_wrappers.FractalZarr, plate_3d: hcs_wrappers.FractalZarr):
    """Test `FractalZarr.get_channels().`"""
    channels_expected = [{'wavelength_id': 'A01_C01', 'label': 'some-label-1',
                          'window': {'min': '0', 'max': '10', 'start': '0', 'end': '10'},
                          'color': '00FFFF'},
                         {'wavelength_id': 'A01_C02', 'label': 'some-label-2',
                          'window': {'min': '0', 'max': '10', 'start': '0', 'end': '10'},
                          'color': '00FFFF'}]
    assert plate_2d.get_channels() == plate_2d.channels
    assert plate_2d.get_channels() == channels_expected
    assert plate_3d.get_channels() == plate_3d.channels
    assert plate_3d.get_channels() == channels_expected

test_get_image_ROI_3d(plate_3d)

Test FractalZarr.get_image_ROI().

Source code in tests/test_hcs_wrappers.py

def test_get_image_ROI_3d(plate_3d: hcs_wrappers.FractalZarr):
    """Test `FractalZarr.get_image_ROI()`."""
    img0a = plate_3d.get_image_ROI(well=None, pyramid_level=2,
                                   upper_left_yx=None,
                                   lower_right_yx=None,
                                   size_yx=None,
                                   as_NumPy=False)
    img0b = plate_3d.get_image_ROI(well='B03', pyramid_level=2,
                                   upper_left_yx=(0, 0),
                                   lower_right_yx=(269, 319),
                                   size_yx=None,
                                   as_NumPy=True)
    assert isinstance(img0a, dask.array.Array)
    assert isinstance(img0b, np.ndarray)
    assert img0a.shape == (2, 3, 270, 320)
    assert (np.array(img0a) == img0b).all()

    with pytest.raises(Exception) as e_info:
        plate_3d.get_image_ROI(well='B03', pyramid_level=1,
                               upper_left_yx=(11, 10),
                               lower_right_yx=None, size_yx=None)

    img1a = plate_3d.get_image_ROI(well='B03', pyramid_level=1,
                                   pyramid_level_coord=0,
                                   upper_left_yx=(22, 20),
                                   lower_right_yx=(44, 40),
                                   size_yx=None,
                                   as_NumPy=True)
    img1b = plate_3d.get_image_ROI(well='B03', pyramid_level=1,
                                   upper_left_yx=(11, 10),
                                   lower_right_yx=None,
                                   size_yx=(11, 10),
                                   as_NumPy=True)
    img1c = plate_3d.get_image_ROI(well='B03', pyramid_level=1,
                                   upper_left_yx=None,
                                   lower_right_yx=(22, 20),
                                   size_yx=(11, 10),
                                   as_NumPy=True)
    assert isinstance(img1a, np.ndarray)
    assert isinstance(img1b, np.ndarray)
    assert isinstance(img1c, np.ndarray)
    assert img1a.shape == (2, 3, 12, 11)
    assert img1b.shape == img1a.shape
    assert img1c.shape == img1a.shape
    assert (img1b == img1a).all()
    assert (img1c == img1a).all()

test_get_image_grid_ROIs_3d(plate_3d)

Test FractalZarr.get_image_grid_ROIs().

Source code in tests/test_hcs_wrappers.py

def test_get_image_grid_ROIs_3d(plate_3d: hcs_wrappers.FractalZarr):
    """Test `FractalZarr.get_image_grid_ROIs().`"""
    # exceptions
    with pytest.raises(Exception) as e_info:
        plate_3d.get_image_grid_ROIs(num_x=2, num_y=2, num_select=5)

    with pytest.raises(Exception) as e_info:
        plate_3d.get_image_grid_ROIs(pyramid_level=2, sample_method='error')

    # sample_method = 'random'                        
    coord_1a, img_1a = plate_3d.get_image_grid_ROIs(well='B03', pyramid_level=2,
                                                    num_x=3, num_y=1, num_select=1,
                                                    sample_method='random', seed=1)
    coord_1b, img_1b = plate_3d.get_image_grid_ROIs(well='B03', pyramid_level=2,
                                                    num_x=3, num_y=1, num_select=1,
                                                    sample_method='random', seed=1)
    coord_2, img_2 = plate_3d.get_image_grid_ROIs(well='B03', pyramid_level=2,
                                                  num_x=3, num_y=1, num_select=1,
                                                  sample_method='random', seed=11)
    coord_3, img_3 = plate_3d.get_image_grid_ROIs(well='B03', pyramid_level=2,
                                                  num_x=8, num_y=8,
                                                  num_select=3,
                                                  sample_method='random', seed=3,
                                                  as_NumPy=True)
    assert len(coord_1a) == 1
    assert coord_1a == coord_1b
    assert len(coord_2) == 1
    assert coord_1a != coord_2
    assert all([isinstance(x, dask.array.Array) for x in img_1a])
    assert all(x.shape == (2, 3, 270, 106) for x in img_1a)
    assert all(x.shape == (2, 3, 270, 106) for x in img_1b)
    assert all(x.shape == (2, 3, 270, 106) for x in img_2)
    assert len(coord_3) == 3
    assert all([isinstance(x, np.ndarray) for x in img_3])
    assert all(x.shape == (2, 3, 33, 40) for x in img_3)

    # sample_method = 'sum'
    coord_4, img_4 = plate_3d.get_image_grid_ROIs(well='B03', pyramid_level=2,
                                                  num_x=3, num_y=1, num_select=3,
                                                  sample_method='sum')
    assert len(coord_4) == 3
    assert all([isinstance(x, dask.array.Array) for x in img_4])
    assert all(x.shape == (2, 3, 270, 106) for x in img_4)

    # sample_method = 'var'
    coord_5, img_5 = plate_3d.get_image_grid_ROIs(well='B03', pyramid_level=2,
                                                  num_x=3, num_y=1, num_select=3,
                                                  sample_method='var')
    assert len(coord_5) == 3
    assert all([isinstance(x, dask.array.Array) for x in img_5])
    assert all(x.shape == (2, 3, 270, 106) for x in img_5)

test_get_image_table_idx(plate_2d)

Test FractalZarr.get_image_table_idx().

Source code in tests/test_hcs_wrappers.py

def test_get_image_table_idx(plate_2d: hcs_wrappers.FractalZarr):
    """Test `FractalZarr.get_image_table_idx()`."""
    with pytest.raises(Exception) as e_info:
        plate_2d.get_image_table_idx(table_name='does-not-exist', table_idx=0)
    img = plate_2d.get_image_table_idx(table_name='FOV_ROI_table',
                                       table_idx=0, well='B03', pyramid_level=2,
                                       as_NumPy=False)
    assert isinstance(img, dask.array.Array)
    assert img.shape == (2, 1, 136, 161)

test_get_label_ROI_2d(plate_2d)

Test FractalZarr.get_label_ROI().

Source code in tests/test_hcs_wrappers.py

def test_get_label_ROI_2d(plate_2d: hcs_wrappers.FractalZarr):
    """Test `FractalZarr.get_label_ROI()`."""
    msk0a = plate_2d.get_label_ROI(label_name='organoids',
                                   well=None, pyramid_level=2,
                                   upper_left_yx=None,
                                   lower_right_yx=None,
                                   size_yx=None,
                                   as_NumPy=False)
    msk0b = plate_2d.get_label_ROI(label_name='organoids',
                                   well='B03', pyramid_level=2,
                                   upper_left_yx=(0, 0),
                                   lower_right_yx=(269, 319),
                                   size_yx=None,
                                   as_NumPy=True)
    assert isinstance(msk0a, dask.array.Array)
    assert isinstance(msk0b, np.ndarray)
    assert msk0a.shape == (1, 270, 320)
    assert (np.array(msk0a) == msk0b).all()

    with pytest.raises(Exception) as e_info:
        plate_2d.get_label_ROI(label_name='organoids',
                               well='B03', pyramid_level=1,
                               upper_left_yx=(11, 10),
                               lower_right_yx=None, size_yx=None)

    with pytest.raises(Exception) as e_info:
        plate_2d.get_label_ROI(label_name='does-not-exist',
                               well='B03', pyramid_level=1,
                               upper_left_yx=(11, 10),
                               size_yx=(10, 10))

    msk1a = plate_2d.get_label_ROI(label_name='organoids',
                                   well='B03', pyramid_level=1,
                                   pyramid_level_coord=0,
                                   upper_left_yx=(22, 20),
                                   lower_right_yx=(44, 40),
                                   size_yx=None,
                                   as_NumPy=True)
    msk1b = plate_2d.get_label_ROI(label_name='organoids',
                                   well='B03', pyramid_level=1,
                                   upper_left_yx=(11, 10),
                                   lower_right_yx=None,
                                   size_yx=(11, 10),
                                   as_NumPy=True)
    msk1c = plate_2d.get_label_ROI(label_name='organoids',
                                   well='B03', pyramid_level=1,
                                   upper_left_yx=None,
                                   lower_right_yx=(22, 20),
                                   size_yx=(11, 10),
                                   as_NumPy=True)
    assert isinstance(msk1a, np.ndarray)
    assert isinstance(msk1b, np.ndarray)
    assert isinstance(msk1c, np.ndarray)
    assert msk1a.shape == (1, 12, 11)
    assert msk1b.shape == msk1a.shape
    assert msk1c.shape == msk1a.shape
    assert (msk1b == msk1a).all()
    assert (msk1c == msk1a).all()

test_get_label_names(plate_2d, plate_3d)

Test FractalZarr.get_label_names().

Source code in tests/test_hcs_wrappers.py

def test_get_label_names(plate_2d: hcs_wrappers.FractalZarr, plate_3d: hcs_wrappers.FractalZarr):
    """Test `FractalZarr.get_label_names().`"""
    assert plate_2d.get_label_names() == ['organoids']
    assert plate_3d.get_label_names() == []

test_get_label_table_idx(plate_2d)

Test FractalZarr.get_table_table_idx().

Source code in tests/test_hcs_wrappers.py

def test_get_label_table_idx(plate_2d: hcs_wrappers.FractalZarr):
    """Test `FractalZarr.get_table_table_idx()`."""
    with pytest.raises(Exception) as e_info:
        plate_2d.get_label_table_idx(label_name='organoids', table_name='does-not-exist', table_idx=0)
    with pytest.raises(Exception) as e_info:
        plate_2d.get_label_table_idx(label_name='does-not-exist', table_name='FOV_ROI_table', table_idx=0)
    msk = plate_2d.get_label_table_idx(label_name='organoids', table_name='FOV_ROI_table',
                                       table_idx=0, well='B03', pyramid_level=2,
                                       as_NumPy=False)
    assert isinstance(msk, dask.array.Array)
    assert msk.shape == (1, 136, 161)

test_get_path(plate_2d, plate_3d)

Test FractalZarr.get_path().

Source code in tests/test_hcs_wrappers.py

def test_get_path(plate_2d: hcs_wrappers.FractalZarr, plate_3d: hcs_wrappers.FractalZarr):
    """Test `FractalZarr.get_path().`"""
    assert plate_2d.get_path() == plate_2d.path
    assert plate_2d.get_path() == 'tests/example_data/plate_ones_mip.zarr'
    assert plate_3d.get_path() == plate_3d.path
    assert plate_3d.get_path() == 'tests/example_data/plate_ones.zarr'

test_get_table(plate_2d)

Test FractalZarr.get_table.

Source code in tests/test_hcs_wrappers.py

def test_get_table(plate_2d: hcs_wrappers.FractalZarr):
    """Test `FractalZarr.get_table`."""
    empty = plate_2d.get_table('does not exist')
    df = plate_2d.get_table('FOV_ROI_table')
    ann = plate_2d.get_table('FOV_ROI_table', as_AnnData=True)
    assert empty is None
    assert isinstance(df, pd.DataFrame)
    assert df.shape == (4, 9)
    assert isinstance(ann, ad.AnnData)
    assert ann.shape == (4, 8)
    assert 'well' in ann.obs
    df2 = plate_2d.get_table('FOV_ROI_table', include_wells=['B03'], as_AnnData=False)
    assert df.equals(df2)

test_get_table_names(plate_2d, plate_3d)

Test FractalZarr.get_table_names().

Source code in tests/test_hcs_wrappers.py

def test_get_table_names(plate_2d: hcs_wrappers.FractalZarr, plate_3d: hcs_wrappers.FractalZarr):
    """Test `FractalZarr.get_table_names().`"""
    assert plate_2d.get_table_names() == plate_2d.table_names
    assert plate_3d.get_table_names() == plate_3d.table_names

test_get_wells(plate_2d, plate_3d)

Test FractalZarr.get_wells().

Source code in tests/test_hcs_wrappers.py

def test_get_wells(plate_2d: hcs_wrappers.FractalZarr, plate_3d: hcs_wrappers.FractalZarr):
    """Test `FractalZarr.get_wells().`"""
    wells_expected = [{'columnIndex': 0, 'path': 'B/03', 'rowIndex': 0}]
    wells_expected_simple = ['B03']
    assert plate_2d.get_wells() == plate_2d.wells
    assert plate_2d.get_wells() == wells_expected
    assert plate_3d.get_wells() == plate_3d.wells
    assert plate_3d.get_wells() == wells_expected
    assert plate_2d.get_wells(simplify=True) == wells_expected_simple
    assert plate_3d.get_wells(simplify=True) == wells_expected_simple

test_missing_channel_attrs(tmpdir)

Test FractalZarr missing channel attributes.

Source code in tests/test_hcs_wrappers.py

def test_missing_channel_attrs(tmpdir: str):
    """Test `FractalZarr` missing channel attributes."""
    # copy zarr fileset
    assert tmpdir.check()
    shutil.copytree('tests/example_data', str(tmpdir) + '/example_data')
    assert tmpdir.join('/example_data/plate_ones_mip.zarr/B/03/0/.zattrs').check()
    # remove omero attributes from copy
    zattr_file = str(tmpdir) + '/example_data/plate_ones_mip.zarr/B/03/0/.zattrs'
    with open(zattr_file) as f:
       zattr = json.load(f)
    del zattr['omero']
    with open(zattr_file, "w") as jsonfile:
        json.dump(zattr, jsonfile, indent=4)
    # test loading
    with pytest.raises(Exception) as e_info:
        hcs_wrappers.FractalZarr(str(tmpdir) + '/example_data/plate_ones_mip.zarr')

test_missing_image_multiscales_attrs(tmpdir)

Test FractalZarr missing multiscales attributes.

Source code in tests/test_hcs_wrappers.py

def test_missing_image_multiscales_attrs(tmpdir: str):
    """Test `FractalZarr` missing multiscales attributes."""
    # copy zarr fileset
    assert tmpdir.check()
    shutil.copytree('tests/example_data', str(tmpdir) + '/example_data')
    assert tmpdir.join('/example_data/plate_ones_mip.zarr/B/03/0/.zattrs').check()
    # remove multiscales attributes from copy
    zattr_file = str(tmpdir) + '/example_data/plate_ones_mip.zarr/B/03/0/.zattrs'
    with open(zattr_file) as f:
       zattr = json.load(f)
    del zattr['multiscales']
    with open(zattr_file, "w") as jsonfile:
        json.dump(zattr, jsonfile, indent=4)
    # test loading
    with pytest.raises(Exception) as e_info:
        hcs_wrappers.FractalZarr(str(tmpdir) + '/example_data/plate_ones_mip.zarr')

test_missing_label_multiscales_attrs(tmpdir)

Test FractalZarr missing multiscales attributes.

Source code in tests/test_hcs_wrappers.py

def test_missing_label_multiscales_attrs(tmpdir: str):
    """Test `FractalZarr` missing multiscales attributes."""
    # copy zarr fileset
    assert tmpdir.check()
    shutil.copytree('tests/example_data', str(tmpdir) + '/example_data')
    assert tmpdir.join('/example_data/plate_ones_mip.zarr/B/03/0/labels/organoids/.zattrs').check()
    # remove multiscales attributes from copy
    zattr_file = str(tmpdir) + '/example_data/plate_ones_mip.zarr/B/03/0/labels/organoids/.zattrs'
    with open(zattr_file) as f:
       zattr = json.load(f)
    del zattr['multiscales']
    with open(zattr_file, "w") as jsonfile:
        json.dump(zattr, jsonfile, indent=4)
    # test loading
    with pytest.raises(Exception) as e_info:
        hcs_wrappers.FractalZarr(str(tmpdir) + '/example_data/plate_ones_mip.zarr')

test_missing_tables(tmpdir)

Test FractalZarr missing tables.

Source code in tests/test_hcs_wrappers.py

def test_missing_tables(tmpdir: str):
    """Test `FractalZarr` missing tables."""
    # copy zarr fileset
    assert tmpdir.check()
    shutil.copytree('tests/example_data', str(tmpdir) + '/example_data')
    assert tmpdir.join('/example_data/plate_ones_mip.zarr/B/03/0/.zattrs').check()
    # remove tables
    shutil.rmtree(str(tmpdir) + '/example_data/plate_ones_mip.zarr/B/03/0/tables')
    # test loading
    plate = hcs_wrappers.FractalZarr(str(tmpdir) + '/example_data/plate_ones_mip.zarr')
    assert plate.table_names == []

test_plate_str(plate_2d, plate_3d)

Test FractalZarr object string representation.

Source code in tests/test_hcs_wrappers.py

def test_plate_str(plate_2d: hcs_wrappers.FractalZarr, plate_3d: hcs_wrappers.FractalZarr):
    """Test `FractalZarr` object string representation."""
    assert str(plate_2d) == repr(plate_2d)
    assert str(plate_3d) == repr(plate_3d)

test_plateset_get_element(plate_set1)

Test FractFmiZarr.get_element().

Source code in tests/test_hcs_wrappers.py

def test_plateset_get_element(plate_set1: hcs_wrappers.FractalZarrSet):
    """Test `FractFmiZarr.get_element()`."""
    assert len(plate_set1) == 2
    assert plate_set1[0] == plate_set1.zarr[0]
    assert plate_set1[plate_set1.zarr_names[1]] == plate_set1.zarr[1]

test_plateset_str(plate_set1)

Test FractalZarrSet object string representation.

Source code in tests/test_hcs_wrappers.py

def test_plateset_str(plate_set1: hcs_wrappers.FractalZarrSet):
    """Test `FractalZarrSet` object string representation."""
    assert str(plate_set1) == repr(plate_set1)

test_plot_plate(plate_2d, tmpdir)

Test plot_plate.

Source code in tests/test_hcs_wrappers.py

def test_plot_plate(plate_2d: hcs_wrappers.FractalZarr, tmpdir: str):
    """Test plot_plate."""
    matplotlib.use('Agg')  # Use the 'Agg' backend, which doesn't need a display
    with warnings.catch_warnings():
        warnings.simplefilter('ignore') # suppress warning due to cannot show FigureCanvas 
        # without mask
        plate_2d.plot_plate(image_name='0',
                            label_name=None,
                            pyramid_level=None,
                            channels=[0],
                            channel_colors=['white'],
                            channel_ranges=[[0.01, 0.99]],
                            z_projection_method='maximum',
                            plate_layout='6well')
        # with mask
        plate_2d.plot_plate(image_name='0',
                            label_name='organoids',
                            pyramid_level=None,
                            channels=[0],
                            channel_colors=['white'],
                            channel_ranges=[[0.01, 0.99]],
                            z_projection_method='maximum',
                            plate_layout='6well')
        # fig_style='brightfield'
        plate_2d.plot_plate(image_name='0',
                            label_name='organoids',
                            pyramid_level=None,
                            fig_style='brightfield',
                            plate_layout='6well')

    plt.savefig(tmpdir.join('output.png'))
    assert True # check if the plotting ran through

test_plot_well(plate_2d, tmpdir)

Test plot_plate.

Source code in tests/test_hcs_wrappers.py

def test_plot_well(plate_2d: hcs_wrappers.FractalZarr, tmpdir: str):
    """Test plot_plate."""
    matplotlib.use('Agg')  # Use the 'Agg' backend, which doesn't need a display
    with warnings.catch_warnings():
        warnings.simplefilter('ignore') # suppress warning due to cannot show FigureCanvas 
        plate_2d.plot_well(well='B03',
                           image_name='0',
                           label_name=None,
                           pyramid_level=None,
                           pyramid_level_coord=None,
                           channels=[0],
                           channel_colors=['white'],
                           channel_ranges=[[0.01, 0.99]],
                           z_projection_method='maximum',
                           scalebar_micrometer=50,
                           scalebar_label=True)
        plate_2d.plot_well(well='B03',
                           image_name='0',
                           label_name='organoids',
                           pyramid_level=None,
                           pyramid_level_coord=None,
                           channels=[0],
                           channel_colors=['white'],
                           channel_ranges=[[0.01, 0.99]],
                           z_projection_method='maximum')
    plt.savefig(tmpdir.join('output.png'))
    assert True # check if the plotting ran through