def add_roi_layer(self, image_info: ImageInfo):
if image_info.roi_info.roi is None:
return
try:
max_num = max(1, image_info.roi_count)
except ValueError:
max_num = 1
roi = image_info.roi_info.alternative.get(
self.image_state.roi_presented, image_info.roi_info.roi)
if self.image_state.only_borders:
data = calculate_borders(
roi.transpose(ORDER_DICT[self._current_order]),
self.image_state.borders_thick // 2,
self.viewer.dims.ndisplay == 2,
).transpose(np.argsort(ORDER_DICT[self._current_order]))
image_info.roi = self.viewer.add_image(
data,
scale=image_info.image.normalized_scaling(),
contrast_limits=[0, max_num],
)
else:
image_info.roi = self.viewer.add_image(
roi,
scale=image_info.image.normalized_scaling(),
contrast_limits=[0, max_num],
name="ROI",
blending="translucent",
)
image_info.roi._interpolation[3] = Interpolation3D.NEAREST
def add_segmentation_layer(self, image_info: ImageInfo):
if image_info.segmentation_info.segmentation is None:
return
try:
max_num = max(1, image_info.segmentation_count)
except ValueError:
max_num = 1
if self.image_state.only_borders:
data = calculate_borders(
image_info.segmentation_info.segmentation,
self.image_state.borders_thick // 2,
self.viewer.dims.ndisplay == 2,
)
image_info.segmentation = self.viewer.add_image(
data,
scale=image_info.image.normalized_scaling(),
contrast_limits=[0, max_num],
)
else:
image_info.segmentation = self.viewer.add_image(
image_info.segmentation_info.segmentation,
scale=image_info.image.normalized_scaling(),
contrast_limits=[0, max_num],
name="segmentation",
blending="translucent",
)
image_info.segmentation._interpolation[3] = Interpolation3D.NEAREST
def test_sizes_3d(self, dtype):
data = np.zeros((1, 10, 20, 30), dtype=dtype)
data[0, 2:-2, 2:-2, 2:-2] = 1
res = calculate_borders(data, 0, False)
data[0, 3:-3, 3:-3, 3:-3] = 0
assert np.all(res == data)
assert res.dtype == dtype
def test_simple_2d(self, dtype):
data = np.zeros((1, 10, 10, 10), dtype=dtype)
data[0, 2:-2, 2:-2, 2:-2] = 1
res = calculate_borders(data, 0, True)
data[:, :, 3:-3, 3:-3] = 0
assert np.all(res == data)
assert res.dtype == dtype
def test_labels_3d(self, num, dtype):
data = np.zeros((1, 10, num * 10, 10), dtype=dtype)
for ind in range(num):
data[0, 2:-2, ind * 10 + 2:ind * 10 + 8, 2:-2] = ind + 1
res = calculate_borders(data, 0, False)
for ind in range(num):
data[0, 3:-3, ind * 10 + 3:ind * 10 + 7, 3:-3] = 0
assert np.all(res == data)
assert res.dtype == dtype
def test_simple_thick_2d(self, dtype):
data = np.zeros((1, 10, 10, 10), dtype=dtype)
data[0, 2:-2, 2:-2, 2:-2] = 1
res = calculate_borders(data, 1, True)
data2 = np.copy(data)
res2 = np.copy(res)
res2[data == 0] = 0
data2[0, :, 4:-4, 4:-4] = 0
assert np.all(res2 == data2)
assert res.dtype == dtype
data[0, 2:-2, 1, 2:-2] = 1
data[0, 2:-2, -2, 2:-2] = 1
data[0, 2:-2, 2:-2, 1] = 1
data[0, 2:-2, 2:-2, -2] = 1
data[0, :, 4:-4, 4:-4] = 0
assert np.all(res == data)
