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_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_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_slicing_atlas_along_z_axis_gets_correct_section_image(z, out):
atlas = Atlas(
volume=np.broadcast_to(np.array([10, 16, 21]), (3, 3, 3)),
resolution_um=1,
)
section = atlas.slice(Plane3D(z=z))
assert np.all(section.image.channels == out)
def test_slicing_atlas_along_y_axis_gets_correct_section_image(y, out):
atlas = Atlas(
volume=np.broadcast_to(np.array([10, 16, 21]),
(3, 3, 3)).swapaxes(1, 2),
resolution_um=1,
)
section = atlas.slice(Plane3D(y=y, rx=90))
assert np.all(section.image.channels == out)
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 = Plane3D()
section = atlas.slice(plane)
assert isinstance(section, Section)
assert section.plane_3d == plane
assert section.plane_2d == Plane2D()
assert section.image.pixel_resolution_um == atlas.resolution_um
assert section.image.channels.shape == (1, 3, 3)
assert section.thickness_um == atlas.resolution_um