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