def test_resample_section_gets_section_with_requested_resolution_and_different_image_size(
repo, section1):
resample_section = UpdateSectionCommand(_repo=repo)
request = UpdateSectionRequest(section_id=section1.id,
steps=[Resample(resolution_um=5)])
result = resample_section(request)
assert result.unwrap().resolution_um == 5
assert result.unwrap().section_image.shape == (3, 3)
def test_register_section_returns_2d_orthogonal_atlas_section_images_at_section_position(
repo, section1):
command = UpdateSectionCommand(_repo=repo)
result = command(UpdateSectionRequest(section_id=section1.id, steps=[]))
data = result.ok()
assert data.coronal_atlas_image.ndim == 2
assert data.axial_atlas_image.ndim == 2
assert data.sagittal_atlas_image.ndim == 2
def test_register_section_returns_error_message_if_no_section_loaded(section1):
repo = Mock(BaseRepo)
repo.get_atlas.return_value = Atlas(volume=np.empty((5, 5, 5)),
resolution_um=10)
repo.get_section.return_value = None
command = UpdateSectionCommand(_repo=repo)
result = command(UpdateSectionRequest(section_id=section1.id, steps=[]))
assert "section not found" in result.value.lower()
def test_reorient_section_sets_new_rotations(repo, section1, plane, si, ap,
lr):
command = UpdateSectionCommand(_repo=repo)
request = UpdateSectionRequest(section_id=section1.id,
steps=[Reorient(plane=plane)])
result = command(request)
data = result.ok()
assert data.rot_longitudinal == si
assert data.rot_anteroposterior == ap
assert data.rot_horizontal == lr
def test_update_section_command_works_on_section_with_matching_id(
repo, section1: Section, section2):
command = UpdateSectionCommand(_repo=repo)
result = command(
UpdateSectionRequest(section_id=section1.id, steps=[Center()]))
assert result.is_ok()
data = result.ok()
if data is not None: # mypy workaround, not sure why only happening here.
assert data.section_id == section1.id
repo.get_section.assert_called_with(id=section1.id)
def test_register_section_returns_error_message_if_no_atlas_loaded(section1):
repo = Mock(BaseRepo)
repo.get_atlas.return_value = None
repo.get_sections.return_value = [
Section.create(
image=Image(channels=np.empty((2, 4, 4)), resolution_um=3.4))
]
command = UpdateSectionCommand(_repo=repo)
result = command(UpdateSectionRequest(section_id=section1.id, steps=[]))
assert "no atlas" in result.value.lower()
def test_update_section_updates_multiple_times_if_given_multiple_commands(
repo, section1):
command = UpdateSectionCommand(_repo=repo)
request = UpdateSectionRequest(section_id=section1.id,
steps=[
Translate(Direction.Right, 30),
Translate(Direction.Right, 400)
])
result = command(request)
data = result.ok()
assert data.right == 2 + 30 + 400
def test_center_atlas_command_centers_section_when_atlas_is_loaded():
section = Section.create(
image=Image(channels=np.empty((2, 4, 4)), resolution_um=3.4),
physical_transform=PhysicalTransformer(x=0, y=0, z=0),
)
repo = Mock(BaseRepo)
repo.get_section.return_value = section
repo.get_atlas.return_value = Atlas(volume=np.empty((3, 3, 3)),
annotation_volume=np.empty((3, 3, 3)),
resolution_um=10)
move_section = UpdateSectionCommand(_repo=repo)
request = UpdateSectionRequest(section_id=section.id, steps=[Center()])
result = move_section(request)
data = result.unwrap()
assert data.superior == 15
assert data.anterior == 15
assert data.right == 15
def test_move_section_to_rotation_rotates_it_and_returns_new_position(
value, axis):
physical_transform = PhysicalTransformer(rx=5, ry=10, rz=2)
section = Section.create(image=Image(channels=np.empty((2, 4, 4)),
resolution_um=3.4),
physical_transform=physical_transform)
repo = Mock(BaseRepo)
repo.get_section.return_value = section
repo.get_atlas.return_value = Atlas(volume=np.empty((5, 5, 5)),
resolution_um=10)
move_section = UpdateSectionCommand(_repo=repo)
request = UpdateSectionRequest(section_id=section.id,
steps=[SetRotation(axis=axis, value=value)])
result = move_section(request)
data = result.unwrap()
assert data.rot_longitudinal == value if axis is Axis.Longitudinal else 5
assert data.rot_anteroposterior == value if axis is Axis.Anteroposterior else 10
assert data.rot_horizontal == value if axis is Axis.Horizontal else 2
def test_relative_move_section_to_position_translates_it_and_returns_new_position(
value, direction):
physical_transform = PhysicalTransformer(x=5, y=10, z=2)
section = Section.create(image=Image(channels=np.empty((2, 4, 4)),
resolution_um=3.4),
physical_transform=physical_transform)
repo = Mock(BaseRepo)
repo.get_section.return_value = section
repo.get_atlas.return_value = Atlas(volume=np.empty((3, 3, 3)),
annotation_volume=np.empty((3, 3, 3)),
resolution_um=10)
move_section = UpdateSectionCommand(_repo=repo)
request = UpdateSectionRequest(
section_id=section.id,
steps=[Translate(direction=direction, value=value)])
result = move_section(request)
data = result.unwrap()
if direction is Direction.Superior:
assert data.superior == 5 + value
elif direction is Direction.Inferior:
assert data.superior == 5 - value
else:
assert data.superior == 5
if direction is Direction.Anterior:
assert data.anterior == 10 + value
elif direction is Direction.Posterior:
assert data.anterior == 10 - value
else:
assert data.anterior == 10
if direction is Direction.Right:
assert data.right == 2 + value
elif direction is Direction.Left:
assert data.right == 2 - value
else:
assert data.right == 2
def test_register_section_gets_section_transform_matrix_when_both_section_and_atlas_are_loaded(
repo, section1):
command = UpdateSectionCommand(_repo=repo)
result = command(UpdateSectionRequest(section_id=section1.id, steps=[]))
assert result.ok().section_transform.shape == (4, 4)
def test_register_section_command_gets_atlas_slice_image_when_both_section_and_atlas_are_loaded(
repo, section1):
command = UpdateSectionCommand(_repo=repo)
result = command(UpdateSectionRequest(section_id=section1.id, steps=[]))
assert result.ok().atlas_slice_image.ndim == 2