def test_add_image_colormap_variants():
"""Test adding image with all valid colormap argument types."""
viewer = ViewerModel()
np.random.seed(0)
data = np.random.random((10, 15))
# as string
assert viewer.add_image(data, colormap='green')
# as string that is valid, but not a default colormap
assert viewer.add_image(data, colormap='cubehelix')
# as tuple
cmap_tuple = ("my_colormap", Colormap(['g', 'm', 'y']))
assert viewer.add_image(data, colormap=cmap_tuple)
# as dict
cmap_dict = {"your_colormap": Colormap(['g', 'r', 'y'])}
assert viewer.add_image(data, colormap=cmap_dict)
# as Colormap instance
blue_cmap = AVAILABLE_COLORMAPS['blue']
assert viewer.add_image(data, colormap=blue_cmap)
# string values must be known colormap types
with pytest.raises(KeyError) as err:
viewer.add_image(data, colormap='nonsense')
assert 'Colormap "nonsense" not found' in str(err.value)
# lists are only valid with channel_axis
with pytest.raises(TypeError) as err:
viewer.add_image(data, colormap=['green', 'red'])
assert "did you mean to specify a 'channel_axis'" in str(err.value)
def test_colormap_equality():
colors = np.array([[0, 0, 0, 1], [0, 1, 0, 1], [0, 0, 1, 1]])
cmap_1 = Colormap(colors, name='testing', controls=[0, 0.75, 1])
cmap_2 = Colormap(colors, name='testing', controls=[0, 0.75, 1])
cmap_3 = Colormap(colors, name='testing', controls=[0, 0.25, 1])
assert cmap_1 == cmap_2
assert cmap_1 != cmap_3
def test_can_accept_napari_colormaps_in_dict():
"""Test that we can accept vispy colormaps in a dictionary"""
colors_a = np.array([[0, 0, 0, 1], [0, 1, 0, 1], [0, 0, 1, 1]])
colors_b = np.array([[0, 0, 0, 1], [1, 0, 0, 1], [0, 0, 1, 1]])
napari_cmap_a = Colormap(colors_a)
napari_cmap_b = Colormap(colors_b)
cmap = ensure_colormap({'a': napari_cmap_a, 'b': napari_cmap_b})
assert isinstance(cmap, Colormap)
np.testing.assert_almost_equal(cmap.colors, colors_a)
assert cmap.name == 'a'
def test_linear_colormap():
"""Test a linear colormap."""
colors = np.array([[0, 0, 0, 1], [0, 1, 0, 1], [0, 0, 1, 1]])
cmap = Colormap(colors, name='testing')
assert cmap.name == 'testing'
assert cmap.interpolation == 'linear'
assert len(cmap.controls) == len(colors)
np.testing.assert_almost_equal(cmap.colors, colors)
np.testing.assert_almost_equal(cmap.map([0.75]), [[0, 0.5, 0.5, 1]])
def test_binned_colormap():
"""Test a binned colormap."""
colors = np.array([[0, 0, 0, 1], [0, 1, 0, 1], [0, 0, 1, 1]])
cmap = Colormap(colors, name='testing', interpolation='zero')
assert cmap.name == 'testing'
assert cmap.interpolation == 'zero'
assert len(cmap.controls) == len(colors) + 1
np.testing.assert_almost_equal(cmap.colors, colors)
np.testing.assert_almost_equal(cmap.map([0.4]), [[0, 1, 0, 1]])
def test_can_accept_napari_colormaps():
"""Test that we can accept napari colormaps."""
colors = np.array([[0, 0, 0, 1], [0, 1, 0, 1], [0, 0, 1, 1]])
napari_cmap = Colormap(colors)
cmap = ensure_colormap(napari_cmap)
assert isinstance(cmap, Colormap)
np.testing.assert_almost_equal(cmap.colors, colors)
def test_wrong_number_control_points():
"""Test wrong number of control points raises an error."""
colors = np.array(
[[0, 0, 0, 1], [0, 0.5, 0, 1], [0, 1, 0, 1], [0, 0, 1, 1]]
)
with pytest.raises(ValueError):
Colormap(colors, name='testing', controls=[0, 0.75, 1])
def test_non_ascending_control_points():
"""Test non ascending control points raises an error."""
colors = np.array(
[[0, 0, 0, 1], [0, 0.5, 0, 1], [0, 1, 0, 1], [0, 0, 1, 1]]
)
with pytest.raises(ValueError):
Colormap(colors, name='testing', controls=[0, 0.75, 0.25, 1])
def test_can_accept_napari_colormap_name_tuple():
"""Test that we can accept napari colormap named type."""
colors = np.array([[0, 0, 0, 1], [0, 1, 0, 1], [0, 0, 1, 1]])
napari_cmap = Colormap(colors)
cmap = ensure_colormap(('special_name', napari_cmap))
assert isinstance(cmap, Colormap)
np.testing.assert_almost_equal(cmap.colors, colors)
assert cmap.name == 'special_name'
from napari.utils.colormaps import (
AVAILABLE_COLORMAPS,
CYMRGB,
MAGENTA_GREEN,
SIMPLE_COLORMAPS,
Colormap,
ensure_colormap,
)
from napari.utils.misc import ensure_iterable, ensure_sequence_of_iterables
base_colormaps = CYMRGB
two_colormaps = MAGENTA_GREEN
green_cmap = SIMPLE_COLORMAPS['green']
red_cmap = SIMPLE_COLORMAPS['red']
blue_cmap = AVAILABLE_COLORMAPS['blue']
cmap_tuple = ("my_colormap", Colormap(['g', 'm', 'y']))
cmap_dict = {"your_colormap": Colormap(['g', 'r', 'y'])}
MULTI_TUPLES = [[0.3, 0.7], [0.1, 0.9], [0.3, 0.9], [0.4, 0.9], [0.2, 0.9]]
# data shape is (15, 10, 5) unless otherwise set
# channel_axis = -1 is implied unless otherwise set
multi_channel_test_data = [
# basic multichannel image
((), {}),
# single channel
((15, 10, 1), {}),
# two channels
((15, 10, 2), {}),
# Test adding multichannel image with color channel set.
((5, 10, 15), {'channel_axis': 0}),
# Survivor -> cyan
# Deceased -> red
SURVIVOR_COLORMAP = np.array([[1.0, 0.0, 0.0, 1.0], [0.0, 1.0, 0.8, 1.0]])
# steal some colors, mwah ha ha...
ID_COLORMAP = AVAILABLE_COLORMAPS['turbo'].colors
ID_COLORMAP = ID_COLORMAP[::4, :]
id_colormap = ModuloColormap(ID_COLORMAP,
controls=colormap_bins(ID_COLORMAP),
interpolation='zero',
name='tracking_id')
state_colormap = Colormap(STATE_COLORMAP,
controls=colormap_bins(STATE_COLORMAP),
interpolation='zero',
name='tracking_state')
survivor_colormap = Colormap(SURVIVOR_COLORMAP,
controls=colormap_bins(SURVIVOR_COLORMAP),
interpolation='zero',
name='tracking_survivors')
colormaps = {
'ID': id_colormap,
'parent': id_colormap,
'root': id_colormap,
'states': state_colormap,
'survivor': survivor_colormap
}
def test_colormap_recreate():
c_map = Colormap("black")
Colormap(**c_map.dict())
