def test_paint():
"""Test painting labels with different square brush sizes."""
np.random.seed(0)
data = np.random.randint(20, size=(10, 15))
data[:10, :10] = 1
layer = Labels(data)
with pytest.warns(FutureWarning):
layer.brush_shape = 'square'
assert np.unique(layer.data[:5, :5]) == 1
assert np.unique(layer.data[5:10, 5:10]) == 1
layer.brush_size = 9
layer.paint([0, 0], 2)
assert np.unique(layer.data[:5, :5]) == 2
assert np.unique(layer.data[5:10, 5:10]) == 1
layer.brush_size = 10
layer.paint([0, 0], 2)
assert np.unique(layer.data[:6, :6]) == 2
assert np.unique(layer.data[6:10, 6:10]) == 1
layer.brush_size = 19
layer.paint([0, 0], 2)
assert np.unique(layer.data[:5, :5]) == 2
assert np.unique(layer.data[5:10, 5:10]) == 2
def test_paint_2d(brush_shape, expected_sum):
"""Test painting labels with circle/square brush."""
data = np.zeros((40, 40))
layer = Labels(data)
layer.brush_size = 12
layer.brush_shape = brush_shape
layer.mode = 'paint'
layer.paint((0, 0), 3)
layer.brush_size = 12
layer.paint((15, 8), 4)
layer.brush_size = 13
layer.paint((30.2, 7.8), 5)
layer.brush_size = 12
layer.paint((39, 39), 6)
layer.brush_size = 20
layer.paint((15, 27), 7)
assert np.sum(layer.data[:8, :8] == 3) == expected_sum[0]
assert np.sum(layer.data[9:22, 2:15] == 4) == expected_sum[1]
assert np.sum(layer.data[24:37, 2:15] == 5) == expected_sum[2]
assert np.sum(layer.data[33:, 33:] == 6) == expected_sum[3]
assert np.sum(layer.data[5:26, 17:38] == 7) == expected_sum[4]
def test_paint():
"""Test painting labels with different circle brush sizes."""
np.random.seed(0)
data = np.random.randint(20, size=(10, 15))
data[:10, :10] = 1
layer = Labels(data)
assert np.unique(layer.data[:5, :5]) == 1
assert np.unique(layer.data[5:10, 5:10]) == 1
layer.brush_size = 9
layer.paint([0, 0], 2)
assert np.unique(layer.data[:4, :4]) == 2
assert np.unique(layer.data[5:10, 5:10]) == 1
layer.brush_size = 10
layer.paint([0, 0], 2)
assert np.unique(layer.data[0:6, 0:3]) == 2
assert np.unique(layer.data[0:3, 0:6]) == 2
assert np.unique(layer.data[6:10, 6:10]) == 1
layer.brush_size = 19
layer.paint([0, 0], 2)
assert np.unique(layer.data[0:4, 0:10]) == 2
assert np.unique(layer.data[0:10, 0:4]) == 2
assert np.unique(layer.data[3:7, 3:7]) == 2
assert np.unique(layer.data[7:10, 7:10]) == 1
def test_paint_2d():
"""Test painting labels with circle brush."""
data = np.zeros((40, 40), dtype=np.uint32)
layer = Labels(data)
layer.brush_size = 12
layer.mode = 'paint'
layer.paint((0, 0), 3)
layer.brush_size = 12
layer.paint((15, 8), 4)
layer.brush_size = 13
layer.paint((30.2, 7.8), 5)
layer.brush_size = 12
layer.paint((39, 39), 6)
layer.brush_size = 20
layer.paint((15, 27), 7)
assert np.sum(layer.data[:8, :8] == 3) == 41
assert np.sum(layer.data[9:22, 2:15] == 4) == 137
assert np.sum(layer.data[24:37, 2:15] == 5) == 137
assert np.sum(layer.data[33:, 33:] == 6) == 41
assert np.sum(layer.data[5:26, 17:38] == 7) == 349
def test_paint(Event, brush_shape, expected_sum):
"""Test painting labels with circle/square brush."""
data = np.ones((20, 20), dtype=np.int32)
layer = Labels(data)
layer.brush_size = 10
assert layer.cursor_size == 10
with pytest.warns(FutureWarning):
layer.brush_shape = brush_shape
layer.mode = 'paint'
layer.selected_label = 3
# Simulate click
event = ReadOnlyWrapper(
Event(type='mouse_press', is_dragging=False, position=(0, 0)))
mouse_press_callbacks(layer, event)
# Simulate drag
event = ReadOnlyWrapper(
Event(type='mouse_move', is_dragging=True, position=(19, 19)))
mouse_move_callbacks(layer, event)
# Simulate release
event = ReadOnlyWrapper(
Event(type='mouse_release', is_dragging=False, position=(19, 19)))
mouse_release_callbacks(layer, event)
# Painting goes from (0, 0) to (19, 19) with a brush size of 10, changing
# all pixels along that path, but none outside it.
assert np.unique(layer.data[:8, :8]) == 3
assert np.unique(layer.data[-8:, -8:]) == 3
assert np.unique(layer.data[:5, -5:]) == 1
assert np.unique(layer.data[-5:, :5]) == 1
assert np.sum(layer.data == 3) == expected_sum
def test_erase(Event, brush_shape, expected_sum):
"""Test erasing labels with different brush shapes."""
data = np.ones((20, 20))
layer = Labels(data)
layer.brush_size = 10
layer.mode = 'erase'
layer.brush_shape = brush_shape
layer.selected_label = 3
layer.position = (0, 0)
# Simulate click
event = ReadOnlyWrapper(Event(type='mouse_press', is_dragging=False))
mouse_press_callbacks(layer, event)
layer.position = (19, 19)
# Simulate drag
event = ReadOnlyWrapper(Event(type='mouse_move', is_dragging=True))
mouse_move_callbacks(layer, event)
# Simulate release
event = ReadOnlyWrapper(Event(type='mouse_release', is_dragging=False))
mouse_release_callbacks(layer, event)
# Painting goes from (0, 0) to (19, 19) with a brush size of 10, changing
# all pixels along that path, but non outside it.
assert np.unique(layer.data[:8, :8]) == 0
assert np.unique(layer.data[-8:, -8:]) == 0
assert np.unique(layer.data[:5, -5:]) == 1
assert np.unique(layer.data[-5:, :5]) == 1
assert np.sum(layer.data == 1) == expected_sum
def test_paint_scale(Event, brush_shape, expected_sum):
"""Test painting labels with circle/square brush when scaled."""
data = np.ones((20, 20))
layer = Labels(data, scale=(2, 2))
layer.brush_size = 20
layer.brush_shape = brush_shape
layer.mode = 'paint'
layer.selected_label = 3
layer.position = (0, 0)
# Simulate click
event = ReadOnlyWrapper(Event(type='mouse_press', is_dragging=False))
mouse_press_callbacks(layer, event)
layer.position = (39, 39)
# Simulate drag
event = ReadOnlyWrapper(Event(type='mouse_move', is_dragging=True))
mouse_move_callbacks(layer, event)
# Simulate release
event = ReadOnlyWrapper(Event(type='mouse_release', is_dragging=False))
mouse_release_callbacks(layer, event)
# Painting goes from (0, 0) to (19, 19) with a brush size of 10, changing
# all pixels along that path, but none outside it.
assert np.unique(layer.data[:8, :8]) == 3
assert np.unique(layer.data[-8:, -8:]) == 3
assert np.unique(layer.data[:5, -5:]) == 1
assert np.unique(layer.data[-5:, :5]) == 1
assert np.sum(layer.data == 3) == expected_sum
def test_undo_redo(
brush_shape,
brush_size,
mode,
selected_label,
preserve_labels,
n_dimensional,
):
blobs = data.binary_blobs(length=64, volume_fraction=0.3, n_dim=3)
layer = Labels(blobs)
data_history = [blobs.copy()]
with pytest.warns(FutureWarning):
layer.brush_shape = brush_shape
layer.brush_size = brush_size
layer.mode = mode
layer.selected_label = selected_label
layer.preserve_labels = preserve_labels
layer.n_edit_dimensions = 3 if n_dimensional else 2
coord = np.random.random((3, )) * (np.array(blobs.shape) - 1)
while layer.data[tuple(coord.astype(int))] == 0 and np.any(layer.data):
coord = np.random.random((3, )) * (np.array(blobs.shape) - 1)
if layer.mode == 'fill':
layer.fill(coord, layer.selected_label)
if layer.mode == 'erase':
layer.paint(coord, 0)
if layer.mode == 'paint':
layer.paint(coord, layer.selected_label)
data_history.append(np.copy(layer.data))
layer.undo()
np.testing.assert_array_equal(layer.data, data_history[0])
layer.redo()
np.testing.assert_array_equal(layer.data, data_history[1])
def test_ndim_paint():
test_array = np.zeros((5, 6, 7, 8), dtype=int)
layer = Labels(test_array)
layer.n_edit_dimensions = 3
with pytest.warns(FutureWarning):
layer.brush_shape = 'circle'
layer.brush_size = 2 # equivalent to 18-connected 3D neighborhood
layer.paint((1, 1, 1, 1), 1)
assert np.sum(layer.data) == 19 # 18 + center
assert not np.any(layer.data[0]) and not np.any(layer.data[2:])
layer.n_edit_dimensions = 2 # 3x3 square
layer._dims_order = [1, 2, 0, 3]
layer.paint((4, 5, 6, 7), 8)
assert len(np.flatnonzero(layer.data == 8)) == 4 # 2D square is in corner
np.testing.assert_array_equal(
test_array[:, 5, 6, :],
np.array([
[0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 8, 8],
[0, 0, 0, 0, 0, 0, 8, 8],
]),
)
def test_brush_size():
"""Test changing brush size."""
np.random.seed(0)
data = np.random.randint(20, size=(10, 15))
layer = Labels(data)
assert layer.brush_size == 10
layer.brush_size = 20
assert layer.brush_size == 20
def test_paint():
"""Test painting labels with different brush sizes."""
np.random.seed(0)
data = np.random.randint(20, size=(10, 15))
data[:10, :10] = 1
layer = Labels(data)
assert np.unique(layer.data[:5, :5]) == 1
assert np.unique(layer.data[5:10, 5:10]) == 1
layer.brush_size = 10
layer.paint([0, 0], 2)
assert np.unique(layer.data[:5, :5]) == 2
assert np.unique(layer.data[5:10, 5:10]) == 1
layer.brush_size = 20
layer.paint([0, 0], 2)
assert np.unique(layer.data[:5, :5]) == 2
assert np.unique(layer.data[5:10, 5:10]) == 2
def test_paint(MouseEvent):
"""Test painting labels with circle brush."""
data = np.ones((20, 20), dtype=np.int32)
layer = Labels(data)
layer.brush_size = 10
assert layer.cursor_size == 10
layer.mode = 'paint'
layer.selected_label = 3
# Simulate click
event = ReadOnlyWrapper(
MouseEvent(
type='mouse_press',
is_dragging=False,
position=(0, 0),
view_direction=None,
dims_displayed=(0, 1),
dims_point=(0, 0),
)
)
mouse_press_callbacks(layer, event)
# Simulate drag
event = ReadOnlyWrapper(
MouseEvent(
type='mouse_move',
is_dragging=True,
position=(19, 19),
view_direction=None,
dims_displayed=(0, 1),
dims_point=(0, 0),
)
)
mouse_move_callbacks(layer, event)
# Simulate release
event = ReadOnlyWrapper(
MouseEvent(
type='mouse_release',
is_dragging=False,
position=(19, 19),
view_direction=None,
dims_displayed=(0, 1),
dims_point=(0, 0),
)
)
mouse_release_callbacks(layer, event)
# Painting goes from (0, 0) to (19, 19) with a brush size of 10, changing
# all pixels along that path, but none outside it.
assert np.unique(layer.data[:8, :8]) == 3
assert np.unique(layer.data[-8:, -8:]) == 3
assert np.unique(layer.data[:5, -5:]) == 1
assert np.unique(layer.data[-5:, :5]) == 1
assert np.sum(layer.data == 3) == 244
def test_paint_2d_xarray():
"""Test the memory usage of painting an xarray indirectly via timeout."""
data = xr.DataArray(np.zeros((3, 3, 1024, 1024), dtype=np.uint32))
layer = Labels(data)
layer.brush_size = 12
layer.mode = 'paint'
layer.paint((1, 1, 512, 512), 3)
assert isinstance(layer.data, xr.DataArray)
assert layer.data.sum() == 411
def test_negative_label():
"""Test negative label values are supported."""
data = np.random.randint(low=-1, high=20, size=(10, 10))
original_data = np.copy(data)
layer = Labels(data)
layer.selected_label = -1
layer.brush_size = 3
layer.paint((5, 5), -1)
assert np.count_nonzero(layer.data == -1) > np.count_nonzero(
original_data == -1)
def test_paint_3d_negative_scale(scale):
labels = np.zeros((3, 5, 11, 11), dtype=int)
labels_layer = Labels(labels,
scale=(1, ) + scale,
translate=(-200, 100, 100))
labels_layer.n_edit_dimensions = 3
labels_layer.brush_size = 8
labels_layer.paint((1, 2, 5, 5), 1)
np.testing.assert_array_equal(np.sum(labels_layer.data, axis=(1, 2, 3)),
[0, 95, 0])
def test_paint_2d_xarray(brush_shape, expected_sum):
"""Test the memory usage of painting an xarray indirectly via timeout."""
data = xr.DataArray(np.zeros((3, 3, 1024, 1024), dtype=np.uint32))
layer = Labels(data)
layer.brush_size = 12
with pytest.warns(FutureWarning):
layer.brush_shape = brush_shape
layer.mode = 'paint'
layer.paint((1, 1, 512, 512), 3)
assert isinstance(layer.data, xr.DataArray)
assert layer.data.sum() == expected_sum
def test_paint_2d_xarray():
"""Test the memory usage of painting an xarray indirectly via timeout."""
now = time.monotonic()
data = xr.DataArray(np.zeros((3, 3, 1024, 1024), dtype=np.uint32))
layer = Labels(data)
layer.brush_size = 12
layer.mode = 'paint'
layer.paint((1, 1, 512, 512), 3)
assert isinstance(layer.data, xr.DataArray)
assert layer.data.sum() == 411
elapsed = time.monotonic() - now
assert elapsed < 1, "test was too slow, computation was likely not lazy"
def test_paint_with_preserve_labels():
"""Test painting labels while preserving existing labels"""
data = np.zeros((15, 10))
data[:3, :3] = 1
layer = Labels(data)
layer.preserve_labels = True
assert np.unique(layer.data[:3, :3]) == 1
layer.brush_size = 9
layer.paint([0, 0], 2)
assert np.unique(layer.data[3:5, 0:5]) == 2
assert np.unique(layer.data[0:5, 3:5]) == 2
assert np.unique(layer.data[:3, :3]) == 1
def test_paint_with_preserve_labels():
"""Test painting labels with square brush while preserving existing labels."""
data = np.zeros((15, 10), dtype=np.uint32)
data[:3, :3] = 1
layer = Labels(data)
with pytest.warns(FutureWarning):
layer.brush_shape = 'square'
layer.preserve_labels = True
assert np.unique(layer.data[:3, :3]) == 1
layer.brush_size = 9
layer.paint([0, 0], 2)
assert np.unique(layer.data[3:5, 0:5]) == 2
assert np.unique(layer.data[0:5, 3:5]) == 2
assert np.unique(layer.data[:3, :3]) == 1
def test_mouse_move():
"""Test painting labels with different brush sizes."""
np.random.seed(0)
data = np.random.randint(20, size=(20, 20))
layer = Labels(data)
layer.brush_size = 10
layer.mode = 'paint'
layer.selected_label = 3
layer._last_cursor_coord = (0, 0)
layer.coordinates = (19, 19)
Event = collections.namedtuple('Event', 'is_dragging')
event = Event(is_dragging=True)
layer.on_mouse_move(event)
assert np.unique(layer.data[:5, :5]) == 3
assert np.unique(layer.data[-5:, -5:]) == 3
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_paint_3d():
"""Test painting labels with circle brush on 3D image."""
data = np.zeros((30, 40, 40), dtype=np.uint32)
layer = Labels(data)
layer.brush_size = 12
layer.mode = 'paint'
# Paint in 2D
layer.paint((10, 10, 10), 3)
# Paint in 3D
layer.n_edit_dimensions = 3
layer.paint((10, 25, 10), 4)
# Paint in 3D, preserve labels
layer.n_edit_dimensions = 3
layer.preserve_labels = True
layer.paint((10, 15, 15), 5)
assert np.sum(layer.data[4:17, 4:17, 4:17] == 3) == 137
assert np.sum(layer.data[4:17, 19:32, 4:17] == 4) == 1189
assert np.sum(layer.data[4:17, 9:32, 9:32] == 5) == 1103
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_paint_3d(brush_shape, expected_sum):
"""Test painting labels with circle/square brush on 3D image."""
data = np.zeros((30, 40, 40))
layer = Labels(data)
layer.brush_size = 12
layer.brush_shape = brush_shape
layer.mode = 'paint'
# Paint in 2D
layer.paint((10, 10, 10), 3)
# Paint in 3D
layer.n_dimensional = True
layer.paint((10, 25, 10), 4)
# Paint in 3D, preserve labels
layer.n_dimensional = True
layer.preserve_labels = True
layer.paint((10, 15, 15), 5)
assert np.sum(layer.data[4:17, 4:17, 4:17] == 3) == expected_sum[0]
assert np.sum(layer.data[4:17, 19:32, 4:17] == 4) == expected_sum[1]
assert np.sum(layer.data[4:17, 9:32, 9:32] == 5) == expected_sum[2]
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
