def test_channel(self, small_cont: ImageContainer, channel: int):
segment(small_cont, copy=False, layer="image", channel=channel)
assert Key.img.segment("watershed") in small_cont
np.testing.assert_array_equal(
list(small_cont[Key.img.segment("watershed")].dims),
["y", "x", f"{small_cont['image'].dims[-1]}:{channel}"])
def test_parallelize(self, small_cont: ImageContainer):
res1 = segment(small_cont, layer="image", n_jobs=1, copy=True)
res2 = segment(small_cont, layer="image", n_jobs=2, copy=True)
np.testing.assert_array_equal(
res1[Key.img.segment("watershed")].values,
res2[Key.img.segment("watershed")].values)
def test_copy(self, small_cont: ImageContainer):
prev_keys = set(small_cont)
res = segment(small_cont, copy=True, layer="image")
assert isinstance(res, ImageContainer)
assert set(small_cont) == prev_keys
assert Key.img.segment("watershed") in res
def test_size(self, small_cont: ImageContainer,
dy: Optional[Union[int, float]], dx: Optional[Union[int,
float]]):
res = segment(small_cont, size=(dy, dx), copy=True)
assert isinstance(res, ImageContainer)
assert res.shape == small_cont.shape
def test_watershed_works(self, size: Optional[int]):
img_orig = np.zeros((100, 200, 30), dtype=np.float64)
img_orig[2:10, 2:10] = 1.0
img_orig[30:34, 10:16] = 1.0
cont = ImageContainer(img_orig, layer="image_0")
segment(
img=cont,
method="watershed",
layer="image_0",
layer_added="segment",
size=size,
channel=0,
thresh=0.5,
)
# check that blobs are in segments
assert np.mean(
cont.data["segment"].values[img_orig[:, :, 0] > 0] > 0) > 0.5
def test_key_added(self, small_cont: ImageContainer,
key_added: Optional[str]):
res = segment(small_cont,
copy=False,
layer="image",
layer_added=key_added)
assert res is None
assert Key.img.segment("watershed",
layer_added=key_added) in small_cont
def test_method(self, small_cont: ImageContainer, method: Union[str,
Callable]):
res = segment(small_cont, method=method, copy=True)
assert isinstance(res, ImageContainer)
assert res.shape == small_cont.shape
if callable(method):
method = SegmentationBackend.CUSTOM.s
assert Key.img.segment(method) in res
if method in ("log", "dog", "dog"):
assert res[Key.img.segment(method)].values.max() <= 1
def test_invalid_layer(self, small_cont: ImageContainer):
with pytest.raises(KeyError,
match=r"Image layer `foobar` not found in"):
segment(small_cont, layer="foobar")