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
