def test_value():
"""Test getting the value of the data at the current coordinates."""
np.random.seed(0)
data = np.random.randint(20, size=(10, 15))
layer = Labels(data)
value = layer.get_value()
assert layer.coordinates == (0, 0)
assert value == data[0, 0]
def test_value_3d(position, view_direction, dims_displayed, world):
"""get_value should return label value in 3D"""
data = np.zeros((20, 20, 20), dtype=int)
data[0:10, 0:10, 0:10] = 1
layer = Labels(data)
layer._slice_dims([0, 0, 0], ndisplay=3)
value = layer.get_value(
position,
view_direction=view_direction,
dims_displayed=dims_displayed,
world=world,
)
assert value == 1
def test_properties():
"""Test adding labels with properties."""
np.random.seed(0)
data = np.random.randint(20, size=(10, 15))
layer = Labels(data)
assert isinstance(layer.properties, dict)
assert len(layer.properties) == 0
properties = {
'class': np.array(['Background'] + [f'Class {i}' for i in range(20)])
}
label_index = {i: i for i in range(len(properties['class']))}
layer = Labels(data, properties=properties)
assert isinstance(layer.properties, dict)
np.testing.assert_equal(layer.properties, properties)
assert layer._label_index == label_index
layer = Labels(data)
layer.properties = properties
assert isinstance(layer.properties, dict)
np.testing.assert_equal(layer.properties, properties)
assert layer._label_index == label_index
current_label = layer.get_value((0, 0))
layer_message = layer.get_status((0, 0))
assert layer_message.endswith(f'Class {current_label - 1}')
properties = {'class': ['Background']}
layer = Labels(data, properties=properties)
layer_message = layer.get_status((0, 0))
assert layer_message.endswith("[No Properties]")
properties = {'class': ['Background', 'Class 12'], 'index': [0, 12]}
label_index = {0: 0, 12: 1}
layer = Labels(data, properties=properties)
layer_message = layer.get_status((0, 0))
assert layer._label_index == label_index
assert layer_message.endswith('Class 12')
layer = Labels(data)
layer.properties = properties
layer_message = layer.get_status((0, 0))
assert layer._label_index == label_index
assert layer_message.endswith('Class 12')
layer = Labels(data)
layer.properties = pd.DataFrame(properties)
layer_message = layer.get_status((0, 0))
assert layer._label_index == label_index
assert layer_message.endswith('Class 12')
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()
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_square(self, n):
"""Time to paint square."""
self.layer.brush_shape = 'square'
self.layer.paint(self.layer.coordinates, self.layer.selected_label)
def time_paint_circle(self, n):
"""Time to paint circle."""
self.layer.brush_shape = 'circle'
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
