def test_slicing_atlas_along_leftright_axis_gets_correct_section_image(right, out):
atlas = Atlas(
volume=np.broadcast_to(np.array([10, 16, 21]), (3, 3, 3)).swapaxes(0, 2),
resolution_um=1,
)
section = atlas.slice(AtlasTransform(right=right, rot_axial=-90))
assert np.all(section.image.channels == out)
def test_slicing_atlas_along_infsup_axis_gets_correct_section_image(superior, out):
atlas = Atlas(
volume=np.broadcast_to(np.array([10, 16, 21]), (3, 3, 3)).swapaxes(1, 2),
resolution_um=1,
)
section = atlas.slice(AtlasTransform(superior=superior, rot_lateral=90))
assert np.all(section.image.channels == out)
def test_slicing_atlas_along_postant_axis_gets_correct_section_image(anterior, out):
atlas = Atlas(
volume=np.broadcast_to(np.array([10, 16, 21]), (3, 3, 3)),
resolution_um=1,
)
section = atlas.slice(AtlasTransform(anterior=anterior))
assert np.all(section.image.channels == out)
def test_section_registration_cuts_correctly_with_diff_resolutions(case):
volume = np.zeros((3, 3, 3))
volume[1, 1, 1] = 1
volume[0, 0, 0] = 2
volume[0, 0, 0] = 2
atlas = Atlas(
volume=volume,
resolution_um=case['atlas_res'],
)
section = Section(
image=ImageData(
channels=np.ones((1, 3, 3)),
pixel_resolution_um=case["section_res"],
),
plane_3d=AtlasTransform(**case["pos"]),
)
atlas_slice = register(section, atlas).image.channels[0]
expected_slice = np.array(case['expected']).astype(float)
try:
assert np.all(np.isclose(atlas_slice, expected_slice))
except:
assert np.all(
atlas_slice ==
expected_slice) # similar, but nicer printout of arrays in pytest
# # different dimensions
# # rotate
# # plane_2d: image origin
# # (get visibility on atlas indices)
def repo():
repo = Mock(BaseSectionRepo)
repo.sections = [
Section(
image=ImageData(channels=np.random.random((2, 3, 4)), pixel_resolution_um=12.),
plane_3d=AtlasTransform(right=5, superior=2, anterior=20),
)
]
return repo
def test_3d_translation_gives_correct_affine_transform(right, superior,
anterior):
expected = [
[1, 0, 0, right],
[0, 1, 0, superior],
[0, 0, 1, anterior],
[0, 0, 0, 1],
]
observed = AtlasTransform(right=right,
superior=superior,
anterior=anterior).affine_transform
assert np.all(np.isclose(observed, expected))
def test_slicing_an_atlas_gets_a_new_section_with_correct_parameters():
atlas = Atlas(
volume=np.broadcast_to(np.array([10, 20, 30]), (3, 3, 3)).swapaxes(0, 2),
resolution_um=1
)
plane = AtlasTransform()
section = atlas.slice(plane)
assert isinstance(section, Section)
assert section.plane_3d == plane
assert section.plane_2d == Image2DTransform()
assert section.image.pixel_resolution_um == atlas.resolution_um
assert section.image.channels.shape == (1, 3, 3)
assert section.thickness_um == atlas.resolution_um
def test_can_get_3d_position_from_2d_pixel_coordinate_in_section(
i, j, right, superior, anterior, pixel_resolution):
section = Section(
image=ImageData(
channels=arange(24).reshape(2, 3, 4),
pixel_resolution_um=pixel_resolution,
),
plane_3d=AtlasTransform(right=right,
superior=superior,
anterior=anterior),
)
x, y, z = section.pos_from_coord(i=i, j=j) # observed 3D positions
assert x == approx((j * pixel_resolution) + right)
assert y == approx((-i * pixel_resolution) + superior)
assert z == approx(anterior)
def test_3d_x_rotation_gives_correct_affine_transform(rot_lateral):
expected = [
[1, 0, 0, 0],
[
0,
np.cos(np.radians(rot_lateral)), -np.sin(np.radians(rot_lateral)),
0
],
[
0,
np.sin(np.radians(rot_lateral)),
np.cos(np.radians(rot_lateral)), 0
],
[0, 0, 0, 1],
]
observed = AtlasTransform(rot_lateral=rot_lateral).affine_transform
assert np.all(np.isclose(observed, expected))
def test_section_registration_to_an_atlas_gets_a_section_that_matches_sections_parameters(
):
section = Section(
image=ImageData(
channels=np.random.random((3, 4, 5)),
pixel_resolution_um=10,
),
plane_2d=Image2DTransform(i=3, j=5, theta=20),
plane_3d=AtlasTransform(right=10, superior=-5, anterior=10),
)
atlas = Atlas(volume=np.random.random((5, 5, 5)), resolution_um=20)
s2 = register(section, atlas)
assert type(s2) is Section
assert s2.image.pixel_resolution_um == section.image.pixel_resolution_um
assert s2.id != section.id and s2 is not section
assert s2.image.width == section.image.width, f"{s2.image.channels.shape}, {section.image.channels.shape}"
assert s2.image.height == section.image.height
assert np.all(np.isclose(s2.affine_transform, section.affine_transform))