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_n_edit_dimensions():
"""Test changing the number of editable dimensions."""
np.random.seed(0)
data = np.random.randint(20, size=(5, 10, 15))
layer = Labels(data)
layer.n_edit_dimensions = 2
with pytest.warns(FutureWarning):
assert layer.n_dimensional is False
layer.n_edit_dimensions = 3
with pytest.warns(FutureWarning):
assert layer.n_dimensional is True
def test_fill_tensorstore():
labels = np.zeros((5, 7, 8, 9), dtype=int)
labels[1, 2:4, 4:6, 4:6] = 1
labels[1, 3:5, 5:7, 6:8] = 2
labels[2, 3:5, 5:7, 6:8] = 3
with TemporaryDirectory(suffix='.zarr') as fout:
labels_temp = zarr.open(
fout,
mode='w',
shape=labels.shape,
dtype=np.uint32,
chunks=(1, 1, 8, 9),
)
labels_temp[:] = labels
labels_ts_spec = {
'driver': 'zarr',
'kvstore': {
'driver': 'file',
'path': fout
},
'path': '',
'metadata': {
'dtype': labels_temp.dtype.str,
'order': labels_temp.order,
'shape': labels.shape,
},
}
data = ts.open(labels_ts_spec, create=False, open=True).result()
layer = Labels(data)
layer.n_edit_dimensions = 3
layer.fill((1, 4, 6, 7), 4)
modified_labels = np.where(labels == 2, 4, labels)
np.testing.assert_array_equal(modified_labels, np.asarray(data))
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_n_edit_dimensions():
"""Test changing the number of editable dimensions."""
np.random.seed(0)
data = np.random.randint(20, size=(5, 10, 15))
layer = Labels(data)
layer.n_edit_dimensions = 2
layer.n_edit_dimensions = 3
def test_ndim_fill():
test_array = np.zeros((5, 5, 5, 5), dtype=int)
test_array[:, 1:3, 1:3, 1:3] = 1
layer = Labels(test_array)
layer.n_edit_dimensions = 3
layer.fill((0, 1, 1, 1), 2)
np.testing.assert_equal(layer.data[0, 1:3, 1:3, 1:3], 2)
np.testing.assert_equal(layer.data[1, 1:3, 1:3, 1:3], 1)
layer.n_edit_dimensions = 4
layer.fill((1, 1, 1, 1), 3)
np.testing.assert_equal(layer.data[0, 1:3, 1:3, 1:3], 2)
np.testing.assert_equal(layer.data[1:, 1:3, 1:3, 1:3], 3)
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_fill_nD_all(MouseEvent):
"""Test filling label nD."""
data = np.ones((20, 20, 20), dtype=np.int32)
data[:5, :5, :5] = 2
data[0, 8:10, 8:10] = 2
data[-5:, -5:, -5:] = 3
layer = Labels(data)
assert np.unique(layer.data[:5, :5, :5]) == 2
assert np.unique(layer.data[-5:, -5:, -5:]) == 3
assert np.unique(layer.data[:5, -5:, -5:]) == 1
assert np.unique(layer.data[-5:, :5, -5:]) == 1
assert np.unique(layer.data[0, 8:10, 8:10]) == 2
layer.n_edit_dimensions = 3
layer.mode = 'fill'
layer.selected_label = 4
# Simulate click
event = ReadOnlyWrapper(
MouseEvent(
type='mouse_press',
is_dragging=False,
position=(0, 0, 0),
view_direction=(1, 0, 0),
dims_displayed=(0, 1),
dims_point=(0, 0),
)
)
mouse_press_callbacks(layer, event)
assert np.unique(layer.data[:5, :5, :5]) == 4
assert np.unique(layer.data[-5:, -5:, -5:]) == 3
assert np.unique(layer.data[:5, -5:, -5:]) == 1
assert np.unique(layer.data[-5:, :5, -5:]) == 1
assert np.unique(layer.data[0, 8:10, 8:10]) == 2
layer.selected_label = 5
# Simulate click
event = ReadOnlyWrapper(
MouseEvent(
type='mouse_press',
is_dragging=False,
position=(0, 19, 19),
view_direction=(1, 0, 0),
dims_displayed=(0, 1),
dims_point=(0, 0, 0),
)
)
mouse_press_callbacks(layer, event)
assert np.unique(layer.data[:5, :5, :5]) == 4
assert np.unique(layer.data[-5:, -5:, -5:]) == 3
assert np.unique(layer.data[:5, -5:, -5:]) == 5
assert np.unique(layer.data[-5:, :5, -5:]) == 5
assert np.unique(layer.data[0, 8:10, 8:10]) == 2
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_paint_3d(brush_shape, expected_sum):
"""Test painting labels with circle/square brush on 3D image."""
data = np.zeros((30, 40, 40), dtype=np.uint32)
layer = Labels(data)
layer.brush_size = 12
with pytest.warns(FutureWarning):
layer.brush_shape = brush_shape
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) == 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_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_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
