def test_cursor_ray_3d_transposed():
"""Test that the cursor works when the displayed
viewer axes have been transposed
"""
# make a mock mouse event
mouse_event_1 = MouseEvent(
pos=[25, 25],
position=[10, 27, 10, 1],
dims_point=[0, 0, 0, 1],
dims_displayed=[0, 2, 1],
view_direction=[1, 0, 0, 0],
)
data = np.zeros((20, 20, 20, 5), dtype=int)
data[0:10, 0:10, 0:10, 1] = 1
labels = Labels(data, scale=(1, 2, 1, 1), translate=(5, 5, 5, 0))
# set the slice to one with data and the view to 3D
labels._slice_dims([0, 0, 0, 1], ndisplay=3)
start_point, end_point = labels.get_ray_intersections(
mouse_event_1.position,
mouse_event_1.view_direction,
mouse_event_1.dims_displayed,
)
np.testing.assert_allclose(start_point, [0, 11, 5, 1])
np.testing.assert_allclose(end_point, [20, 11, 5, 1])
def test_get_value_ray_2d():
"""_get_value_ray currently only returns None in 2D
(i.e., it shouldn't be used for 2D).
"""
# make a mock mouse event
mouse_event = MouseEvent(
pos=[25, 25],
position=[5, 5],
dims_point=[1, 10, 0, 0],
dims_displayed=[2, 3],
view_direction=[1, 0, 0],
)
data = np.zeros((5, 20, 20, 20), dtype=int)
data[1, 0:10, 0:10, 0:10] = 1
labels = Labels(data, scale=(1, 2, 1, 1), translate=(5, 5, 5))
# set the dims to the slice with labels, but 2D
labels._slice_dims([1, 10, 0, 0], ndisplay=2)
value = labels._get_value_ray(
start_point=np.empty([]),
end_point=np.empty([]),
dims_displayed=mouse_event.dims_displayed,
)
assert value is None
def test_cursor_ray_3d():
# make a mock mouse event
mouse_event_1 = MouseEvent(
pos=[25, 25],
position=[1, 10, 27, 10],
dims_point=[1, 0, 0, 0],
dims_displayed=[1, 2, 3],
view_direction=[0, 1, 0, 0],
)
data = np.zeros((5, 20, 20, 20), dtype=int)
data[1, 0:10, 0:10, 0:10] = 1
labels = Labels(data, scale=(1, 1, 2, 1), translate=(5, 5, 5))
# set the slice to one with data and the view to 3D
labels._slice_dims([1, 0, 0, 0], ndisplay=3)
# axis 0 : [0, 20], bounding box extents along view axis, [1, 0, 0]
# click is transformed: (value - translation) / scale
# axis 1: click at 27 in world coords -> (27 - 5) / 2 = 11
# axis 2: click at 10 in world coords -> (10 - 5) / 1 = 5
start_point, end_point = labels.get_ray_intersections(
mouse_event_1.position,
mouse_event_1.view_direction,
mouse_event_1.dims_displayed,
)
np.testing.assert_allclose(start_point, [1, 0, 11, 5])
np.testing.assert_allclose(end_point, [1, 20, 11, 5])
# click in the background
mouse_event_2 = MouseEvent(
pos=[25, 25],
position=[1, 10, 65, 10],
dims_point=[1, 0, 0, 0],
dims_displayed=[1, 2, 3],
view_direction=[0, 1, 0, 0],
)
start_point, end_point = labels.get_ray_intersections(
mouse_event_2.position,
mouse_event_2.view_direction,
mouse_event_2.dims_displayed,
)
assert start_point is None
assert end_point is None
# click in a slice with no labels
mouse_event_3 = MouseEvent(
pos=[25, 25],
position=[0, 10, 27, 10],
dims_point=[0, 0, 0, 0],
dims_displayed=[1, 2, 3],
view_direction=[0, 1, 0, 0],
)
labels._slice_dims([0, 0, 0, 0], ndisplay=3)
start_point, end_point = labels.get_ray_intersections(
mouse_event_3.position,
mouse_event_3.view_direction,
mouse_event_3.dims_displayed,
)
np.testing.assert_allclose(start_point, [0, 0, 11, 5])
np.testing.assert_allclose(end_point, [0, 20, 11, 5])
def test_get_value_ray_3d_transposed():
"""Test using _get_value_ray to interrogate labels in 3D
with the dimensions trasposed.
"""
# make a mock mouse event
mouse_event = MouseEvent(
pos=[25, 25],
position=[10, 5, 5, 1],
dims_point=[0, 0, 0, 1],
dims_displayed=[1, 3, 2],
view_direction=[1, 0, 0, 0],
)
data = np.zeros((5, 20, 20, 20), dtype=int)
data[1, 0:10, 0:10, 0:10] = 1
labels = Labels(data, scale=(1, 2, 1, 1), translate=(0, 5, 5, 5))
# set the dims to the slice with labels
labels._slice_dims((1, 0, 0, 0), ndisplay=3, order=(0, 1, 3, 2))
labels.set_view_slice()
value = labels._get_value_ray(
start_point=np.array([1, 0, 5, 5]),
end_point=np.array([1, 20, 5, 5]),
dims_displayed=mouse_event.dims_displayed,
)
assert value == 1
def test_value_3d(position, view_direction, dims_displayed, world):
"""get_value should return label value in 3D"""
data = np.zeros((20, 20, 20), dtype=int)
data[0:10, 0:10, 0:10] = 1
layer = Labels(data)
layer._slice_dims([0, 0, 0], ndisplay=3)
value = layer.get_value(
position,
view_direction=view_direction,
dims_displayed=dims_displayed,
world=world,
)
assert value == 1
def test_3D_labels():
"""Test instantiating Labels layer with random 3D data."""
shape = (6, 10, 15)
np.random.seed(0)
data = np.random.randint(20, size=shape)
layer = Labels(data)
assert np.all(layer.data == data)
assert layer.ndim == len(shape)
np.testing.assert_array_equal(layer.extent.data[1] + 1, shape)
assert layer._data_view.shape == shape[-2:]
assert layer.editable is True
layer._slice_dims(ndisplay=3)
assert layer._ndisplay == 3
assert layer.editable is False
assert layer.mode == 'pan_zoom'
def test_paint_3d(MouseEvent):
"""Test filling label nD."""
data = np.zeros((21, 21, 21), dtype=np.int32)
data[10, 10, 10] = 1
layer = Labels(data)
layer._slice_dims(point=(0, 0, 0), ndisplay=3)
layer.n_edit_dimensions = 3
layer.mode = 'paint'
layer.selected_label = 4
layer.brush_size = 3
# Simulate click
event = ReadOnlyWrapper(
MouseEvent(
type='mouse_press',
is_dragging=False,
position=(0.1, 0, 0),
view_direction=np.full(3, np.sqrt(3)),
dims_displayed=(0, 1, 2),
dims_point=(0, 0, 0),
)
)
mouse_press_callbacks(layer, event)
np.testing.assert_array_equal(np.unique(layer.data), [0, 4])
num_filled = np.bincount(layer.data.ravel())[4]
assert num_filled > 1
layer.mode = 'erase'
# Simulate click
event = ReadOnlyWrapper(
MouseEvent(
type='mouse_press',
is_dragging=False,
position=(0, 10, 10),
view_direction=(1, 0, 0),
dims_displayed=(0, 1, 2),
dims_point=(0, 0, 0),
)
)
mouse_press_callbacks(layer, event)
new_num_filled = np.bincount(layer.data.ravel())[4]
assert new_num_filled < num_filled
def test_get_value_ray_3d():
"""Test using _get_value_ray to interrogate labels in 3D"""
# make a mock mouse event
mouse_event = MouseEvent(
pos=[25, 25],
position=[10, 5, 5],
dims_point=[1, 0, 0, 0],
dims_displayed=[1, 2, 3],
view_direction=[1, 0, 0],
)
data = np.zeros((5, 20, 20, 20), dtype=int)
data[1, 0:10, 0:10, 0:10] = 1
labels = Labels(data, scale=(1, 2, 1, 1), translate=(5, 5, 5))
# set the dims to the slice with labels
labels._slice_dims([1, 0, 0, 0], ndisplay=3)
value = labels._get_value_ray(
start_point=np.array([1, 0, 5, 5]),
end_point=np.array([1, 20, 5, 5]),
dims_displayed=mouse_event.dims_displayed,
)
assert value == 1
# check with a ray that only goes through background
value = labels._get_value_ray(
start_point=np.array([1, 0, 15, 15]),
end_point=np.array([1, 20, 15, 15]),
dims_displayed=mouse_event.dims_displayed,
)
assert value is None
# set the dims to a slice without labels
labels._slice_dims([0, 0, 0, 0], ndisplay=3)
value = labels._get_value_ray(
start_point=np.array([0, 0, 5, 5]),
end_point=np.array([0, 20, 5, 5]),
dims_displayed=mouse_event.dims_displayed,
)
assert value is None
def test_erase_3d_undo_empty(MouseEvent):
"""Nothing should be added to undo queue when clicks fall outside data."""
data = np.zeros((20, 20, 20), dtype=np.int32)
data[10, :, :] = 1
layer = Labels(data)
layer.brush_size = 5
layer.mode = 'erase'
layer._slice_dims(point=(0, 0, 0), ndisplay=3)
layer.n_edit_dimensions = 3
# Simulate click, outside data
event = ReadOnlyWrapper(
MouseEvent(
type='mouse_press',
is_dragging=False,
position=(-1, -1, -1),
view_direction=(1, 0, 0),
dims_displayed=(0, 1, 2),
dims_point=(0, 0, 0),
)
)
mouse_press_callbacks(layer, event)
# Simulate release
event = ReadOnlyWrapper(
MouseEvent(
type='mouse_release',
is_dragging=False,
position=(-1, -1, -1),
view_direction=(1, 0, 0),
dims_displayed=(0, 1, 2),
dims_point=(0, 0, 0),
)
)
mouse_release_callbacks(layer, event)
# Undo queue should be empty
assert len(layer._undo_history) == 0
def test_erase_3d_undo(MouseEvent):
"""Test erasing labels in 3D then undoing the erase.
Specifically, this test checks that undo is correctly filled even
when a click and drag starts outside of the data volume.
"""
data = np.zeros((20, 20, 20), dtype=np.int32)
data[10, :, :] = 1
layer = Labels(data)
layer.brush_size = 5
layer.mode = 'erase'
layer._slice_dims(point=(0, 0, 0), ndisplay=3)
layer.n_edit_dimensions = 3
# Simulate click
event = ReadOnlyWrapper(
MouseEvent(
type='mouse_press',
is_dragging=False,
position=(-1, -1, -1),
view_direction=(1, 0, 0),
dims_displayed=(0, 1, 2),
dims_point=(0, 0, 0),
)
)
mouse_press_callbacks(layer, event)
# Simulate drag. Note: we need to include top left and bottom right in the
# drag or there are no coordinates to interpolate
event = ReadOnlyWrapper(
MouseEvent(
type='mouse_move',
is_dragging=True,
position=(-1, 0.1, 0.1),
view_direction=(1, 0, 0),
dims_displayed=(0, 1, 2),
dims_point=(0, 0, 0),
)
)
mouse_move_callbacks(layer, event)
event = ReadOnlyWrapper(
MouseEvent(
type='mouse_move',
is_dragging=True,
position=(-1, 18.9, 18.9),
view_direction=(1, 0, 0),
dims_displayed=(0, 1, 2),
dims_point=(0, 0, 0),
)
)
mouse_move_callbacks(layer, event)
# Simulate release
event = ReadOnlyWrapper(
MouseEvent(
type='mouse_release',
is_dragging=False,
position=(-1, 21, 21),
view_direction=(1, 0, 0),
dims_displayed=(0, 1, 2),
dims_point=(0, 0, 0),
)
)
mouse_release_callbacks(layer, event)
# Erasing goes from (-1, -1, -1) to (-1, 21, 21), should split the labels
# into two sections. Undoing should work and reunite the labels to one
# square
assert ndi.label(layer.data)[1] == 2
layer.undo()
assert ndi.label(layer.data)[1] == 1
