def test_nonexistent_image_coords_raise_error_and_doesnt_if_exists(i, j):
section = Section(image=ImageData(channels=arange(180).reshape(2, 3, 30),
pixel_resolution_um=1), )
if i < 0 or i >= section.image.height or j < 0 or j >= section.image.width:
with pytest.raises(ValueError):
section.pos_from_coord(i=i, j=j)
else:
assert section.pos_from_coord(i=i, j=j)
def test_section_recenter_sets_shift_to_half_the_width_and_height(
width, height):
section = Section(image=ImageData(channels=np.random.random((3, height,
width)),
pixel_resolution_um=123))
assert section.plane_2d.x == 0 and section.plane_2d.y == 0
section2 = section.recenter()
assert section2.plane_2d.x == approx(
-width / 2) and section2.plane_2d.y == approx(-height / 2)
def test_can_get_3d_position_from_2d_pixel_coordinate_in_section(
i, j, dx, dy, dz, pixel_resolution):
section = Section(
image=ImageData(
channels=arange(24).reshape(2, 3, 4),
pixel_resolution_um=pixel_resolution,
),
plane_3d=Plane3D(x=dx, y=dy, z=dz),
)
x, y, z = section.pos_from_coord(i=i, j=j) # observed 3D positions
assert x == approx((j * 1 / pixel_resolution) + dx)
assert y == approx((-i * 1 / pixel_resolution) + dy)
assert z == approx(dz)
def test_can_get_correct_3d_position_with_image_shifts_and_planar_rotations(
j, pixel_resolution, x_shift, y_shift, theta):
section = Section(
image=ImageData(channels=arange(2400).reshape(2, 30, 40),
pixel_resolution_um=pixel_resolution),
plane_2d=Image2DTransform(i=x_shift, j=y_shift, theta=theta),
)
x, y, z = section.pos_from_coord(i=0, j=j)
assert x == approx(
(pixel_resolution) * (j * cos(radians(theta)) + x_shift))
assert y == approx(
(pixel_resolution) * (j * sin(radians(theta)) + y_shift))
assert z == 0
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_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.arange(12).reshape(2, 3, 2),
pixel_resolution_um=12), )
]
return repo
def repo():
repo = Mock(BaseSectionRepo)
repo.sections = [
Section(image=ImageData(channels=np.random.random((2, 3, 4)),
pixel_resolution_um=20.))
]
return repo
def test_section_origin_set_sets_shift_to_half_half_and_shift_matrix_to_half_width_height(
width, height):
section = Section(image=ImageData(channels=np.random.random((3, height,
width)),
pixel_resolution_um=120))
assert section.plane_2d.i == 0 and section.plane_2d.j == 0
section2 = section.set_image_origin_to_center()
res = section2.image.pixel_resolution_um
height, width = section2.image.height, section2.image.width
assert section2.plane_2d.i == -0.5 and section2.plane_2d.j == -0.5
expected_shift_matrix = np.array([
[res, 0, 0, -res * height / 2],
[0, res, 0, -res * width / 2],
[0, 0, 1, 0],
[0, 0, 0, 1],
])
assert np.all(np.isclose(section2.shift_matrix, expected_shift_matrix))
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 slice(self, plane: AtlasTransform) -> Section:
new_volume = affine_transform(self.volume,
matrix=plane.affine_transform,
cval=0.)
slice_image = new_volume[:, :, 0][np.newaxis, :, :]
return Section(image=ImageData(channels=slice_image,
pixel_resolution_um=self.resolution_um),
plane_3d=plane,
thickness_um=self.resolution_um)
def test_repo_overwrites_existing_section(repo, section1: Section):
assert len(repo.sections) == 0
repo.save_section(section=section1)
assert len(repo.sections) == 1
repo.save_section(section=section1)
assert len(repo.sections) == 1
section_moved = section1.translate(right=3)
repo.save_section(section=section_moved)
assert len(repo.sections) == 1
def __call__(self, filename: str) -> None: # type: ignore
log = lambda msg: print(msg,
section,
section.affine_transform,
section.image.affine_transform,
(section.image.height, section.image.width),
sep="\n",
end="\n\n")
slice_image = self._reader.read(filename=filename)
section = Section(image=slice_image)
log("Loaded")
section = section.set_image_origin_to_center()
log("Origin Set to Center")
section = section.resample(resolution_um=10)
log("Resampled")
self._repo.save_section(section=section)
self.section_loaded.emit(image=section.image.channels[0],
transform=section.affine_transform)
def register(section: Section, atlas: Atlas) -> Section:
width, height = section.image.width, section.image.height
inds = inds_homog(height=height, width=width)
transform = np.linalg.inv(atlas.affine_transform) @ section.affine_transform
brightness_3d = _register(inds, volume=atlas.volume, transform=transform)
registered_slice = section.with_new_image(
ImageData(
channels=brightness_3d.reshape(1, height, width),
pixel_resolution_um=section.image.pixel_resolution_um,
)
)
return registered_slice
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=Plane2D(x=3, y=5, theta=20),
plane_3d=Plane3D(x=10, y=-5, z=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
assert s2.image.height == section.image.height
assert np.all(np.isclose(s2.affine_transform, section.affine_transform))
def __call__(self, filename: str) -> None: # type: ignore
slice_image = self._reader.read(filename=filename)
section = Section(image=slice_image).recenter()
self._repo.save_section(section=section)
self.section_loaded.emit(image=section.image.channels[0],
transform=section.affine_transform)
def test_resample_section_gets_new_section_with_resampled_image():
section = Section(image=ImageData(channels=np.random.random((3, 4, 4)),
pixel_resolution_um=12))
section2 = section.resample(resolution_um=24)
assert isinstance(section2, Section)
assert section2.image.pixel_resolution_um == 24
def section2():
return Section(image=ImageData(
channels=np.arange(12).reshape(2, 3, 2),
pixel_resolution_um=12,
), )