def test_n_dimensional():
"""Test setting n_dimensional flag for 2D and 4D data."""
shape = (10, 2)
np.random.seed(0)
data = 20 * np.random.random(shape)
layer = Points(data)
assert layer.n_dimensional is False
layer.n_dimensional = True
assert layer.n_dimensional is True
layer = Points(data, n_dimensional=True)
assert layer.n_dimensional is True
shape = (10, 4)
data = 20 * np.random.random(shape)
layer = Points(data)
assert layer.n_dimensional is False
layer.n_dimensional = True
assert layer.n_dimensional is True
layer = Points(data, n_dimensional=True)
assert layer.n_dimensional is True
def test_write(mock_pm: PluginManager):
# saving an image without a writer goes straight to npe2.write
# it will use our plugin writer
image = Image(np.random.rand(20, 20), name='ex_img')
_npe2.write_layers('some_file.tif', [image])
mock_pm.commands.get.assert_called_once_with(f'{PLUGIN_NAME}.my_writer')
# points won't trigger our sample writer
mock_pm.commands.get.reset_mock()
points = Points(np.random.rand(20, 2), name='ex_points')
_npe2.write_layers('some_file.tif', [points])
mock_pm.commands.get.assert_not_called()
# calling _npe2.write_layers with a specific writer contribution should
# directly execute the writer.exec with arguments appropriate for the
# writer spec (single or multi-writer)
mock_pm.commands.get.reset_mock()
writer = mock_pm.get_manifest(PLUGIN_NAME).contributions.writers[0]
writer = MagicMock(wraps=writer)
writer.exec.return_value = ['']
assert _npe2.write_layers('some_file.tif', [points], writer=writer) == ['']
mock_pm.commands.get.assert_not_called()
expected_args = ('some_file.tif', *points.as_layer_data_tuple()[:2])
writer.exec.assert_called_once_with(args=expected_args)
def test_empty_points_with_properties():
""" Test instantiating an empty Points layer with properties
See: https://github.com/napari/napari/pull/1069
"""
properties = {
'label': np.array(['label1', 'label2']),
'cont_prop': np.array([0], dtype=np.float),
}
pts = Points(properties=properties)
current_props = {k: v[0] for k, v in properties.items()}
np.testing.assert_equal(pts.current_properties, current_props)
# verify the property datatype is correct
assert pts.properties['cont_prop'].dtype == np.float
# add two points and verify the default property was applied
pts.add([10, 10])
pts.add([20, 20])
props = {
'label': np.array(['label1', 'label1']),
'cont_prop': np.array([0, 0], dtype=np.float),
}
np.testing.assert_equal(pts.properties, props)
def test_color_cycle_dict(attribute):
"""Test setting edge/face color with a color cycle dict"""
data = np.array([[0, 0], [100, 0], [0, 100]])
properties = {'my_colors': [2, 6, 3]}
points_kwargs = {
'properties': properties,
f'{attribute}_color': 'my_colors',
f'{attribute}_color_cycle': {1: 'green', 2: 'red', 3: 'blue'},
}
layer = Points(data, **points_kwargs)
color_cycle_map = getattr(layer, f'{attribute}_color_cycle_map')
np.testing.assert_allclose(color_cycle_map[2], [1, 0, 0, 1]) # 2 is red
np.testing.assert_allclose(color_cycle_map[3], [0, 0, 1, 1]) # 3 is blue
np.testing.assert_allclose(color_cycle_map[6], [1, 1, 1, 1]) # 6 is white
def update_points(self):
if self.settings.points is not None:
self.points_view_button.setVisible(True)
if self.points_layer is None or self.points_layer not in self.viewer.layers:
self.points_layer = Points(
self.settings.points,
scale=self.settings.image.normalized_scaling())
self.viewer.add_layer(self.points_layer)
else:
self.points_layer.data = self.settings.points
self.points_layer.scale = self.settings.image.normalized_scaling(
)
elif self.points_layer is not None and self.points_layer in self.viewer.layers:
self.points_view_button.setVisible(False)
self.points_layer.data = np.empty((0, 4))
def test_empty_layer_with_face_colormap():
"""Test creating an empty layer where the face color is a colormap
See: https://github.com/napari/napari/pull/1069
"""
default_properties = {'point_type': np.array([1.5], dtype=float)}
layer = Points(
properties=default_properties,
face_color='point_type',
face_colormap='gray',
)
assert layer.face_color_mode == 'colormap'
# verify the current_face_color is correct
face_color = np.array([1, 1, 1, 1])
np.testing.assert_allclose(layer._face.current_color, face_color)
def test_empty_layer_with_edge_colormap():
""" Test creating an empty layer where the face color is a colormap
See: https://github.com/napari/napari/pull/1069
"""
default_properties = {'point_type': np.array([1.5], dtype=np.float)}
layer = Points(
properties=default_properties,
edge_color='point_type',
edge_colormap='grays',
)
assert layer.edge_color_mode == 'colormap'
# verify the current_face_color is correct
edge_color = np.array([1, 1, 1, 1])
assert np.all(layer._current_edge_color == edge_color)
def test_view_data():
coords = np.array([[0, 1, 1], [0, 2, 2], [1, 3, 3], [3, 3, 3]])
layer = Points(coords)
layer.dims.set_point(0, 0)
assert np.all(
layer._view_data == coords[np.ix_([0, 1], layer.dims.displayed)]
)
layer.dims.set_point(0, 1)
assert np.all(
layer._view_data == coords[np.ix_([2], layer.dims.displayed)]
)
layer.dims.ndisplay = 3
assert np.all(layer._view_data == coords)
def test_thumbnail_with_n_points_greater_than_max():
"""Test thumbnail generation with n_points > _max_points_thumbnail
see: https://github.com/napari/napari/pull/934
"""
# 2D
max_points = Points._max_points_thumbnail * 2
bigger_data = np.random.randint(10, 100, (max_points, 2))
big_layer = Points(bigger_data)
big_layer._update_thumbnail()
assert big_layer.thumbnail.shape == big_layer._thumbnail_shape
# #3D
bigger_data_3d = np.random.randint(10, 100, (max_points, 3))
bigger_layer_3d = Points(bigger_data_3d)
bigger_layer_3d.dims.ndisplay = 3
bigger_layer_3d._update_thumbnail()
assert bigger_layer_3d.thumbnail.shape == bigger_layer_3d._thumbnail_shape
def test_push_button(qtbot):
"""Make sure the QtModePushButton works with callbacks"""
layer = Points()
def set_test_prop():
layer.test_prop = True
btn = QtModePushButton(layer,
'test_button',
slot=set_test_prop,
tooltip='tooltip')
assert btn.property('mode') == 'test_button'
assert btn.toolTip() == 'tooltip'
btn.click()
qtbot.wait(50)
assert layer.test_prop
def test_message():
"""Test converting value and coords to message."""
shape = (10, 2)
np.random.seed(0)
data = 20 * np.random.random(shape)
data[-1] = [0, 0]
layer = Points(data)
value = layer.get_value()
msg = layer.get_message(layer.coordinates, value)
assert type(msg) == str
layer.data = layer.data + 5
value = layer.get_value()
msg = layer.get_message(layer.coordinates, value)
assert type(msg) == str
def layers():
"""Fixture that supplies a layers list for testing.
Returns
-------
napari.components.LayerList
The desired napari LayerList.
"""
np.random.seed(0)
list_of_layers = [
Image(np.random.rand(20, 20)),
Labels(np.random.randint(10, size=(20, 2))),
Points(np.random.rand(20, 2)),
Shapes(np.random.rand(10, 2, 2)),
Vectors(np.random.rand(10, 2, 2)),
]
return LayerList(list_of_layers)
def test_add_colormap(attribute):
"""Test directly adding a vispy Colormap object"""
shape = (10, 2)
np.random.seed(0)
data = 20 * np.random.random(shape)
annotations = {'point_type': _make_cycled_properties([0, 1.5], shape[0])}
color_kwarg = f'{attribute}_color'
colormap_kwarg = f'{attribute}_colormap'
args = {color_kwarg: 'point_type', colormap_kwarg: 'viridis'}
layer = Points(
data,
properties=annotations,
**args,
)
setattr(layer, f'{attribute}_colormap', get_colormap('gray'))
layer_colormap = getattr(layer, f'{attribute}_colormap')
assert layer_colormap[0] == 'unknown_colormap'
def test_view_colors():
coords = [[0, 1, 1], [0, 2, 2], [1, 3, 3], [3, 3, 3]]
face_color = np.array([[1, 0, 0, 1], [0, 1, 0, 1], [0, 0, 1, 1],
[0, 0, 1, 1]])
edge_color = np.array([[0, 0, 1, 1], [1, 0, 0, 1], [0, 1, 0, 1],
[0, 0, 1, 1]])
layer = Points(coords, face_color=face_color, edge_color=edge_color)
layer._slice_dims([0, slice(None), slice(None)])
assert np.all(layer._view_face_color == face_color[[0, 1]])
assert np.all(layer._view_edge_color == edge_color[[0, 1]])
layer._slice_dims([1, slice(None), slice(None)])
assert np.all(layer._view_face_color == face_color[[2]])
assert np.all(layer._view_edge_color == edge_color[[2]])
# view colors should return empty array if there are no points
layer._slice_dims([2, slice(None), slice(None)])
assert len(layer._view_face_color) == 0
assert len(layer._view_edge_color) == 0
def test_slice_data():
data = [
(10, 2, 4),
(10 + 2 * 1e-7, 4, 6),
(8, 1, 7),
(10.1, 7, 2),
(10 - 2 * 1e-7, 1, 6),
]
layer = Points(data)
assert len(layer._slice_data((8, slice(None), slice(None)))[0]) == 1
assert len(layer._slice_data((10, slice(None), slice(None)))[0]) == 3
assert (len(
layer._slice_data((10 + 2 * 1e-12, slice(None), slice(None)))[0]) == 3)
assert len(layer._slice_data((10.1, slice(None), slice(None)))[0]) == 1
def layer(request):
"""Parameterized fixture that supplies a layer for testing.
Parameters
----------
request : _pytest.fixtures.SubRequest
The pytest request object
Returns
-------
napari.layers.Layer
The desired napari Layer.
"""
np.random.seed(0)
if request.param == 'image':
data = np.random.rand(20, 20)
return Image(data)
elif request.param == 'labels':
data = np.random.randint(10, size=(20, 20))
return Labels(data)
elif request.param == 'points':
data = np.random.rand(20, 2)
return Points(data)
elif request.param == 'shapes':
data = [
np.random.rand(2, 2),
np.random.rand(2, 2),
np.random.rand(6, 2),
np.random.rand(6, 2),
np.random.rand(2, 2),
]
shape_type = ['ellipse', 'line', 'path', 'polygon', 'rectangle']
return Shapes(data, shape_type=shape_type)
elif request.param == 'shapes-rectangles':
data = np.random.rand(7, 4, 2)
return Shapes(data)
elif request.param == 'vectors':
data = np.random.rand(20, 2, 2)
return Vectors(data)
else:
return None
def test_blending():
"""Test setting layer blending."""
np.random.seed(0)
data = 20 * np.random.random((10, 2))
layer = Points(data)
assert layer.blending == 'translucent'
layer.blending = 'additive'
assert layer.blending == 'additive'
layer = Points(data, blending='additive')
assert layer.blending == 'additive'
layer.blending = 'opaque'
assert layer.blending == 'opaque'
def test_visiblity():
"""Test setting layer visiblity."""
np.random.seed(0)
data = 20 * np.random.random((10, 2))
layer = Points(data)
assert layer.visible is True
layer.visible = False
assert layer.visible is False
layer = Points(data, visible=False)
assert layer.visible is False
layer.visible = True
assert layer.visible is True
def test_opacity():
"""Test setting layer opacity."""
np.random.seed(0)
data = 20 * np.random.random((10, 2))
layer = Points(data)
assert layer.opacity == 1.0
layer.opacity = 0.5
assert layer.opacity == 0.5
layer = Points(data, opacity=0.6)
assert layer.opacity == 0.6
layer.opacity = 0.3
assert layer.opacity == 0.3
def test_is_color_mapped():
shape = (10, 2)
np.random.seed(0)
data = 20 * np.random.random(shape)
annotations = {'point_type': np.array(['A', 'B'] * int((shape[0] / 2)))}
layer = Points(data, properties=annotations)
# giving the name of an annotation should return True
assert layer._is_color_mapped('point_type')
# giving a list should return false (i.e., could be an RGBA color)
assert not layer._is_color_mapped([1, 1, 1, 1])
# giving an ndarray should return false (i.e., could be an RGBA color)
assert not layer._is_color_mapped(np.array([1, 1, 1, 1]))
# give an invalid color argument
with pytest.raises(ValueError):
layer._is_color_mapped((123, 323))
def test_add_color_cycle_to_empty_layer(attribute):
"""Test adding a point to an empty layer when edge/face color is a color cycle
See: https://github.com/napari/napari/pull/1069
"""
default_properties = {'point_type': np.array(['A'])}
color_cycle = ['red', 'blue']
points_kwargs = {
'properties': default_properties,
f'{attribute}_color': 'point_type',
f'{attribute}_color_cycle': color_cycle,
}
layer = Points(**points_kwargs)
# verify the current_edge_color is correct
expected_color = transform_color(color_cycle[0])[0]
color_manager = getattr(layer, f'_{attribute}')
current_color = color_manager.current_color
np.testing.assert_allclose(current_color, expected_color)
# add a point
layer.add([10, 10])
props = {'point_type': np.array(['A'])}
expected_color = np.array([[1, 0, 0, 1]])
np.testing.assert_equal(layer.properties, props)
attribute_color = getattr(layer, f'{attribute}_color')
np.testing.assert_allclose(attribute_color, expected_color)
# add a point with a new property
layer.selected_data = []
layer.current_properties = {'point_type': np.array(['B'])}
layer.add([12, 12])
new_color = np.array([0, 0, 1, 1])
expected_color = np.vstack((expected_color, new_color))
new_properties = {'point_type': np.array(['A', 'B'])}
attribute_color = getattr(layer, f'{attribute}_color')
np.testing.assert_allclose(attribute_color, expected_color)
np.testing.assert_equal(layer.properties, new_properties)
class Points2DSuite:
"""Benchmarks for the Points layer with 2D data"""
params = [2**i for i in range(4, 18, 2)]
def setup(self, n):
np.random.seed(0)
self.data = np.random.random((n, 2))
self.layer = Points(self.data)
def time_create_layer(self, n):
"""Time to create layer."""
Points(self.data)
def time_refresh(self, n):
"""Time to refresh view."""
self.layer.refresh()
def time_set_view_slice(self, n):
"""Time to set view slice."""
self.layer._set_view_slice()
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 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_view_colors():
coords = [[0, 1, 1], [0, 2, 2], [1, 3, 3], [3, 3, 3]]
face_color = np.array([[1, 0, 0, 1], [0, 1, 0, 1], [0, 0, 1, 1],
[0, 0, 1, 1]])
edge_color = np.array([[0, 0, 1, 1], [1, 0, 0, 1], [0, 1, 0, 1],
[0, 0, 1, 1]])
layer = Points(coords, face_color=face_color, edge_color=edge_color)
layer.dims.set_point(0, 0)
print(layer.face_color)
print(layer._view_face_color)
assert np.all(layer._view_face_color == face_color[[0, 1]])
assert np.all(layer._view_edge_color == edge_color[[0, 1]])
layer.dims.set_point(0, 1)
assert np.all(layer._view_face_color == face_color[[2]])
assert np.all(layer._view_edge_color == edge_color[[2]])
# view colors should return empty array if there are no points
layer.dims.set_point(0, 2)
assert len(layer._view_face_color) == 0
assert len(layer._view_edge_color) == 0
def test_adding_points():
"""Test adding Points data."""
shape = (10, 2)
np.random.seed(0)
data = 20 * np.random.random(shape)
layer = Points(data)
assert len(layer.data) == 10
coord = [20, 20]
layer.add(coord)
assert len(layer.data) == 11
assert np.all(layer.data[10] == coord)
# the added point should be selected
assert layer.selected_data == {10}
# test adding multiple points
coords = [[10, 10], [15, 15]]
layer.add(coords)
assert len(layer.data) == 13
assert np.all(layer.data[11:, :] == coords)
# test that the last added points can be deleted
layer.remove_selected()
np.testing.assert_equal(layer.data, np.vstack((data, coord)))
def test_set_text_with_kwarg_dict(properties):
text_kwargs = {
'text': 'type: {point_type}',
'color': [0, 0, 0, 1],
'rotation': 10,
'translation': [5, 5],
'anchor': 'upper_left',
'size': 10,
'visible': True,
}
shape = (10, 2)
np.random.seed(0)
data = 20 * np.random.random(shape)
layer = Points(data, properties=copy(properties), text=text_kwargs)
expected_text = ['type: ' + v for v in properties['point_type']]
np.testing.assert_equal(layer.text.values, expected_text)
for property, value in text_kwargs.items():
if property == 'text':
continue
layer_value = getattr(layer._text, property)
np.testing.assert_equal(layer_value, value)
def create_known_points_layer():
"""Create points layer with known coordinates
Returns
-------
layer : napari.layers.Points
Points layer.
n_points : int
Number of points in the points layer
known_non_point : list
Data coordinates that are known to contain no points. Useful during
testing when needing to guarantee no point is clicked on.
"""
data = [[1, 3], [8, 4], [10, 10], [15, 4]]
known_non_point = [20, 30]
n_points = len(data)
layer = Points(data, size=1)
assert np.all(layer.data == data)
assert layer.ndim == 2
assert len(layer.data) == n_points
assert len(layer.selected_data) == 0
return layer, n_points, known_non_point
def test_adding_points():
"""Test adding Points data."""
shape = (10, 2)
np.random.seed(0)
data = 20 * np.random.random(shape)
layer = Points(data)
assert len(layer.data) == 10
coord = [20, 20]
layer.add(coord)
assert len(layer.data) == 11
assert np.all(layer.data[10] == coord)
# the added point should be selected
assert layer.selected_data == {10}
# test adding multiple points
coords = [[10, 10], [15, 15]]
layer.add(coords)
assert len(layer.data) == 13
assert np.all(layer.data[11:, :] == coords)
def test_changing_modes():
"""Test changing modes."""
shape = (10, 2)
np.random.seed(0)
data = 20 * np.random.random(shape)
layer = Points(data)
assert layer.mode == 'pan_zoom'
assert layer.interactive is True
layer.mode = 'add'
assert layer.mode == 'add'
layer.mode = 'select'
assert layer.mode == 'select'
assert layer.interactive is False
layer.mode = 'pan_zoom'
assert layer.mode == 'pan_zoom'
assert layer.interactive is True
with pytest.raises(ValueError):
layer.mode = 'not_a_mode'
def test_adding_properties(attribute):
"""Test adding properties to an existing layer"""
shape = (10, 2)
np.random.seed(0)
data = 20 * np.random.random(shape)
layer = Points(data)
# add properties
properties = {'point_type': _make_cycled_properties(['A', 'B'], shape[0])}
layer.properties = properties
np.testing.assert_equal(layer.properties, properties)
# add properties as a dataframe
properties_df = pd.DataFrame(properties)
layer.properties = properties_df
np.testing.assert_equal(layer.properties, properties)
# add properties as a dictionary with list values
properties_list = {
'point_type': list(_make_cycled_properties(['A', 'B'], shape[0]))
}
layer.properties = properties_list
assert isinstance(layer.properties['point_type'], np.ndarray)
# removing a property that was the _*_color_property should give a warning
color_manager = getattr(layer, f'_{attribute}')
color_manager.color_properties = {
'name': 'point_type',
'values': np.empty(0),
'current_value': 'A',
}
properties_2 = {
'not_point_type': _make_cycled_properties(['A', 'B'], shape[0])
}
with pytest.warns(RuntimeWarning):
layer.properties = properties_2
def _make_points_layer(self, points, name, **kwargs):
layer = Points(points, name=name, n_dimensional=True, **kwargs)
self._init_layer(layer)
