class Labels2DSuite: """Benchmarks for the Labels layer with 2D data""" params = [2**i for i in range(4, 13)] def setup(self, n): np.random.seed(0) self.data = np.random.randint(20, size=(n, n)) self.layer = Labels(self.data) def time_create_layer(self, n): """Time to create layer.""" Labels(self.data) def time_set_view_slice(self, n): """Time to set view slice.""" self.layer._set_view_slice() def time_refresh(self, n): """Time to refresh view.""" self.layer.refresh() def time_update_thumbnail(self, n): """Time to update thumbnail.""" self.layer._update_thumbnail() def time_get_value(self, n): """Time to get current value.""" self.layer.get_value((0, ) * 2) def time_raw_to_displayed(self, n): """Time to convert raw to displayed.""" self.layer._raw_to_displayed(self.layer._data_raw) def time_paint_square(self, n): """Time to paint square.""" self.layer.brush_shape = 'square' self.layer.paint((0, ) * 2, self.layer.selected_label) def time_paint_circle(self, n): """Time to paint circle.""" self.layer.brush_shape = 'circle' self.layer.paint((0, ) * 2, self.layer.selected_label) def time_fill(self, n): """Time to fill.""" self.layer.fill( (0, ) * 2, 1, self.layer.selected_label, ) def mem_layer(self, n): """Memory used by layer.""" return self.layer def mem_data(self, n): """Memory used by raw data.""" return self.data
def test_switching_display_func_during_slicing(): label_array = (5e6 * np.ones((2, 2, 2))).astype(np.uint64) label_array[0, :, :] = [[0, 1], [2, 3]] layer = Labels(label_array) layer._dims_point = (1, 0, 0) layer._set_view_slice() assert layer._color_lookup_func == layer._lookup_with_low_discrepancy_image assert layer._all_vals.size < 1026
def test_negative_label_slicing(): """Test negative label color doesn't change during slicing.""" data = np.array([[[0, 1], [-1, -1]], [[100, 100], [-1, -2]]]) layer = Labels(data) assert tuple(layer.get_color(1)) != tuple(layer.get_color(-1)) layer._dims_point = (1, 0, 0) layer._set_view_slice() assert tuple(layer.get_color(-1)) != tuple(layer.get_color(100)) assert tuple(layer.get_color(-2)) != tuple(layer.get_color(100))
class Labels3DSuite: """Benchmarks for the Labels layer with 3D data.""" params = [2**i for i in range(4, 11)] def setup(self, n): np.random.seed(0) self.data = np.random.randint(20, size=(n, n, n)) self.layer = Labels(self.data) def time_create_layer(self, n): """Time to create layer.""" Labels(self.data) def time_set_view_slice(self, n): """Time to set view slice.""" self.layer._set_view_slice() def time_refresh(self, n): """Time to refresh view.""" self.layer.refresh() def time_update_thumbnail(self, n): """Time to update thumbnail.""" self.layer._update_thumbnail() def time_get_value(self, n): """Time to get current value.""" self.layer.get_value() def time_save_history(self, n): """Time to save history.""" self.layer._save_history() def time_raw_to_displayed(self, n): """Time to convert raw to displayed.""" self.layer._raw_to_displayed(self.layer._data_raw) def time_paint(self, n): """Time to paint.""" self.layer.paint(self.layer.coordinates, self.layer.selected_label) def time_fill(self, n): """Time to fill.""" self.layer.fill( self.layer.coordinates, self.layer._value, self.layer.selected_label, ) def mem_layer(self, n): """Memory used by layer.""" return self.layer def mem_data(self, n): """Memory used by raw data.""" return self.data
class Labels3DSuite: """Benchmarks for the Labels layer with 3D data.""" params = [2**i for i in range(4, 11)] def setup(self, n): if "CI" in os.environ and n > 512: raise NotImplementedError("Skip on CI (not enough memory)") np.random.seed(0) self.data = np.random.randint(20, size=(n, n, n)) self.layer = Labels(self.data) def time_create_layer(self, n): """Time to create layer.""" Labels(self.data) def time_set_view_slice(self, n): """Time to set view slice.""" self.layer._set_view_slice() def time_refresh(self, n): """Time to refresh view.""" self.layer.refresh() def time_update_thumbnail(self, n): """Time to update thumbnail.""" self.layer._update_thumbnail() def time_get_value(self, n): """Time to get current value.""" self.layer.get_value((0, ) * 3) def time_raw_to_displayed(self, n): """Time to convert raw to displayed.""" self.layer._raw_to_displayed(self.layer._slice.image.raw) def time_paint_circle(self, n): """Time to paint circle.""" self.layer.paint((0, ) * 3, self.layer.selected_label) def time_fill(self, n): """Time to fill.""" self.layer.fill( (0, ) * 3, 1, self.layer.selected_label, ) def mem_layer(self, n): """Memory used by layer.""" return self.layer def mem_data(self, n): """Memory used by raw data.""" return self.data
def test_negative_label_doesnt_flicker(): data = np.array([ [[0, 5], [0, 5]], [[-1, 5], [-1, 5]], [[-1, 6], [-1, 6]], ]) layer = Labels(data) layer._dims_point = (1, 0, 0) layer._set_view_slice() # this is expected to fail: -1 doesn't trigger an index error in # layer._all_vals, it instead just wraps to 5, the previous max label. assert tuple(layer.get_color(-1)) != tuple(layer.get_color(5)) minus_one_color_original = tuple(layer.get_color(-1)) layer.dims_point = (2, 0, 0) layer._set_view_slice() # this is also expected to fail: when we switch layers, we see the 6 # label, which causes an index error, which triggers a recalculation of # the label colors. Now -1 is seen so it is taken into account in the # indexing calculation, and changes color assert tuple(layer.get_color(-1)) == minus_one_color_original