def test_changing_modes(): """Test changing modes.""" np.random.seed(0) data = np.random.randint(20, size=(10, 15)) layer = Labels(data) assert layer.mode == 'pan_zoom' assert layer.interactive is True layer.mode = 'fill' assert layer.mode == 'fill' assert layer.interactive is False layer.mode = 'paint' assert layer.mode == 'paint' assert layer.interactive is False layer.mode = 'pick' assert layer.mode == 'pick' assert layer.interactive is False layer.mode = 'pan_zoom' assert layer.mode == 'pan_zoom' assert layer.interactive is True layer.mode = 'paint' assert layer.mode == 'paint' layer.editable = False assert layer.mode == 'pan_zoom' assert layer.editable is False
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_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_fill(Event): """Test filling label.""" data = np.ones((20, 20)) data[:5, :5] = 2 data[-5:, -5:] = 3 layer = Labels(data) assert np.unique(layer.data[:5, :5]) == 2 assert np.unique(layer.data[-5:, -5:]) == 3 assert np.unique(layer.data[:5, -5:]) == 1 assert np.unique(layer.data[-5:, :5]) == 1 layer.mode = 'fill' layer.position = (0, 0) layer.selected_label = 4 # Simulate click event = ReadOnlyWrapper(Event(type='mouse_press', is_dragging=False)) mouse_press_callbacks(layer, event) assert np.unique(layer.data[:5, :5]) == 4 assert np.unique(layer.data[-5:, -5:]) == 3 assert np.unique(layer.data[:5, -5:]) == 1 assert np.unique(layer.data[-5:, :5]) == 1 layer.position = (19, 19) layer.selected_label = 5 # Simulate click event = ReadOnlyWrapper(Event(type='mouse_press', is_dragging=False)) mouse_press_callbacks(layer, event) assert np.unique(layer.data[:5, :5]) == 4 assert np.unique(layer.data[-5:, -5:]) == 5 assert np.unique(layer.data[:5, -5:]) == 1 assert np.unique(layer.data[-5:, :5]) == 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_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_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_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_fill_nD_plane(MouseEvent): """Test filling label nD plane.""" 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.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[0, :5, :5]) == 4 assert np.unique(layer.data[1:5, :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.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[0, :5, :5]) == 4 assert np.unique(layer.data[1:5, :5, :5]) == 2 assert np.unique(layer.data[-5:, -5:, -5:]) == 3 assert np.unique(layer.data[1:5, -5:, -5:]) == 1 assert np.unique(layer.data[-5:, :5, -5:]) == 1 assert np.unique(layer.data[0, -5:, -5:]) == 5 assert np.unique(layer.data[0, :5, -5:]) == 5 assert np.unique(layer.data[0, 8:10, 8:10]) == 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_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_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_pick(Event): """Test picking label.""" data = np.ones((20, 20), dtype=np.int32) data[:5, :5] = 2 data[-5:, -5:] = 3 layer = Labels(data) assert layer.selected_label == 1 layer.mode = 'pick' # Simulate click event = ReadOnlyWrapper( Event(type='mouse_press', is_dragging=False, position=(0, 0))) mouse_press_callbacks(layer, event) assert layer.selected_label == 2 # Simulate click event = ReadOnlyWrapper( Event(type='mouse_press', is_dragging=False, position=(19, 19))) mouse_press_callbacks(layer, event) assert layer.selected_label == 3
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_fill_nD_all(Event): """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_dimensional = True layer.mode = 'fill' layer.selected_label = 4 # Simulate click event = ReadOnlyWrapper( Event(type='mouse_press', is_dragging=False, position=(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:]) == 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( Event(type='mouse_press', is_dragging=False, position=(0, 19, 19))) 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_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
def test_cursor_size_with_negative_scale(): layer = Labels(np.zeros((5, 5), dtype=int), scale=[-1, -1]) layer.mode = 'paint' assert layer.cursor_size > 0