def test_padding_top_bottom(self, small_cont_1c: ImageContainer):
dim1, dim2, _ = small_cont_1c["image"].data.shape
crop = small_cont_1c.crop_center(dim1, dim2 // 2, dim1 // 2)
data = crop["image"].data
np.testing.assert_array_equal(data[dim1 // 2:, :], 0)
crop = small_cont_1c.crop_center(0, dim2 // 2, dim1 // 2)
data = crop["image"].data
np.testing.assert_array_equal(data[:dim2 // 2, :], 0)
def test_padding_left_right(self, small_cont_1c: ImageContainer):
dim1, dim2, _ = small_cont_1c["image"].data.shape
crop = small_cont_1c.crop_center(dim1 // 2, 0, dim1 // 2)
data = crop["image"].data
np.testing.assert_array_equal(data[:, :dim2 // 2], 0)
crop = small_cont_1c.crop_center(dim1 // 2, dim2, dim1 // 2)
data = crop["image"].data
np.testing.assert_array_equal(data[:, dim2 // 2:], 0)
def test_padding_bottom_left(self, small_cont_1c: ImageContainer):
crop = small_cont_1c.crop_center(small_cont_1c.shape[1], 0, 10)
data = crop["image"].data
assert crop.shape == (21, 21)
np.testing.assert_array_equal(data[10:, :10], 0)
np.testing.assert_array_equal(data[:10, 10:] != 0, True)
def test_crop_center_radius(self, small_cont_1c: ImageContainer,
ry: Optional[Union[int, float]],
rx: Optional[Union[int, float]]):
crop = small_cont_1c.crop_center(0, 0, radius=(ry, rx))
sy = int(ry * small_cont_1c.shape[0]) if isinstance(ry, float) else ry
sx = int(rx * small_cont_1c.shape[1]) if isinstance(rx, float) else rx
assert crop.shape == (2 * sy + 1, 2 * sx + 1)
def test_plot_crop_corner(self, qtbot, adata: AnnData, napari_cont: ImageContainer):
viewer = napari_cont.crop_center(500, 500, radius=250).interactive(adata)
bdata = viewer.adata
cnt = viewer._controller
cnt.add_points(bdata.obs_vector(bdata.var_names[42]), layer_name="foo")
viewer.screenshot(dpi=DPI)
def test_crop_smapp(self, cont_dot: ImageContainer):
crop = cont_dot.crop_center(
x=50,
y=20,
radius=0,
cval=5,
)
np.testing.assert_array_equal(crop.data["image_0"].shape, (1, 1, 10))
np.testing.assert_array_equal(crop.data["image_0"][0, 0, :3],
[10, 11, 12])
assert crop.data["image_0"].dtype == np.uint8
def test_crop_scale(self, cont_dot: ImageContainer):
# crop with scaling
mask = np.random.randint(low=0, high=10, size=cont_dot.shape)
cont_dot.add_img(mask, layer="image_1", channel_dim="mask")
crop = cont_dot.crop_center(y=50, x=20, radius=10, cval=5, scale=0.5)
assert "image_0" in crop
assert "image_1" in crop
np.testing.assert_array_equal(crop.data["image_0"].shape,
(21 // 2, 21 // 2, 10))
np.testing.assert_array_equal(crop.data["image_1"].shape,
(21 // 2, 21 // 2, 1))
def test_crop_mask_circle(self, cont_dot: ImageContainer):
# crop with mask_circle
crop = cont_dot.crop_center(
y=20,
x=50,
radius=5,
cval=5,
mask_circle=True,
)
np.testing.assert_array_equal(crop.data["image_0"][1, 0, :], 5)
np.testing.assert_array_equal(crop.data["image_0"][2, 2, :], 0)
np.testing.assert_array_equal(crop.data["image_0"][7, 7, :], 0)
np.testing.assert_array_equal(crop.data["image_0"][9, 9, :], 5)
def test_crop_multiple_images(self, cont_dot: ImageContainer):
mask = np.random.randint(low=0, high=10, size=cont_dot.shape)
cont_dot.add_img(mask, layer="image_1", channel_dim="mask")
crop = cont_dot.crop_center(
y=50,
x=20,
radius=0,
cval=5,
)
assert "image_0" in crop
assert "image_1" in crop
np.testing.assert_array_equal(crop.data["image_0"].shape, (1, 1, 10))
np.testing.assert_array_equal(crop.data["image_1"].shape, (1, 1, 1))
def test_big_crop(self, cont_dot: ImageContainer):
crop = cont_dot.crop_center(
y=50,
x=20,
radius=150,
cval=5,
)
np.testing.assert_array_equal(crop.data["image_0"].shape,
(301, 301, 10))
# check that values outside of img are padded with 5
np.testing.assert_array_equal(crop.data["image_0"][0, 0, 0], 5)
np.testing.assert_array_equal(crop.data["image_0"][-1, -1, 0], 5)
assert crop.data["image_0"].dtype == np.uint8
# compare with crop_corner
crop2 = cont_dot.crop_corner(y=-100, x=-130, size=301, cval=5)
np.testing.assert_array_equal(crop2.data["image_0"],
crop.data["image_0"])
