def test_clim_range():
"""Test setting color limits range."""
shapes = [(40, 20), (20, 10), (10, 5)]
np.random.seed(0)
data = [np.random.random(s) for s in shapes]
layer = Pyramid(data)
assert layer._clim_range[0] >= 0
assert layer._clim_range[1] <= 1
assert layer._clim_range[0] < layer._clim_range[1]
# If all data is the same value the clim_range and clim defaults to [0, 1]
shapes = [(40, 20), (20, 10), (10, 5)]
data = [np.zeros(s) for s in shapes]
layer = Pyramid(data)
assert layer._clim_range == [0, 1]
assert layer.clim == [0.0, 1.0]
# Set clim_range as keyword argument
shapes = [(40, 20), (20, 10), (10, 5)]
data = [np.random.random(s) for s in shapes]
layer = Pyramid(data, clim_range=[0, 2])
assert layer._clim_range == [0, 2]
# Set clim and clim_range as keyword arguments
shapes = [(40, 20), (20, 10), (10, 5)]
data = [np.random.random(s) for s in shapes]
layer = Pyramid(data, clim=[0.3, 0.6], clim_range=[0, 2])
assert layer.clim == [0.3, 0.6]
assert layer._clim_range == [0, 2]
def test_thumbnail():
"""Test the image thumbnail for square data."""
shapes = [(40, 40), (20, 20), (10, 10)]
np.random.seed(0)
data = [np.random.random(s) for s in shapes]
layer = Pyramid(data)
layer._update_thumbnail()
assert layer.thumbnail.shape == layer._thumbnail_shape
def test_message():
"""Test converting value and coords to message."""
shapes = [(40, 20), (20, 10), (10, 5)]
np.random.seed(0)
data = [np.random.random(s) for s in shapes]
layer = Pyramid(data)
msg = layer.get_message()
assert type(msg) == str
def test_value():
"""Test getting the value of the data at the current coordinates."""
shapes = [(40, 20), (20, 10), (10, 5)]
np.random.seed(0)
data = [np.random.random(s) for s in shapes]
layer = Pyramid(data)
coord, value = layer.get_value()
assert np.all(coord == [0, 0])
assert value == data[-1][0, 0]
def test_xml_list():
"""Test the xml generation."""
shapes = [(40, 20), (20, 10), (10, 5)]
np.random.seed(0)
data = [np.random.random(s) for s in shapes]
layer = Pyramid(data)
xml = layer.to_xml_list()
assert type(xml) == list
assert len(xml) == 1
assert type(xml[0]) == Element
def test_metadata():
"""Test setting image metadata."""
shapes = [(40, 20), (20, 10), (10, 5)]
np.random.seed(0)
data = [np.random.random(s) for s in shapes]
layer = Pyramid(data)
assert layer.metadata == {}
layer = Pyramid(data, metadata={'unit': 'cm'})
assert layer.metadata == {'unit': 'cm'}
def test_interpolation():
"""Test setting image interpolation mode."""
shapes = [(40, 20), (20, 10), (10, 5)]
np.random.seed(0)
data = [np.random.random(s) for s in shapes]
layer = Pyramid(data)
assert layer.interpolation == 'nearest'
layer = Pyramid(data, interpolation='bicubic')
assert layer.interpolation == 'bicubic'
layer.interpolation = 'bilinear'
assert layer.interpolation == 'bilinear'
def test_name():
"""Test setting layer name."""
shapes = [(40, 20), (20, 10), (10, 5)]
np.random.seed(0)
data = [np.random.random(s) for s in shapes]
layer = Pyramid(data)
assert layer.name == 'Pyramid'
layer = Pyramid(data, name='random')
assert layer.name == 'random'
layer.name = 'img'
assert layer.name == 'img'
def test_contrast_limits_range():
"""Test setting color limits range."""
shapes = [(40, 20), (20, 10), (10, 5)]
np.random.seed(0)
data = [np.random.random(s) for s in shapes]
layer = Pyramid(data)
assert layer._contrast_limits_range[0] >= 0
assert layer._contrast_limits_range[1] <= 1
assert layer._contrast_limits_range[0] < layer._contrast_limits_range[1]
# If all data is the same value the contrast_limits_range and contrast_limits defaults to [0, 1]
shapes = [(40, 20), (20, 10), (10, 5)]
data = [np.zeros(s) for s in shapes]
layer = Pyramid(data)
assert layer._contrast_limits_range == [0, 1]
assert layer.contrast_limits == [0.0, 1.0]
def test_non_rgb_image():
"""Test forcing Pyramid layer to be 3D and not multichannel."""
shapes = [(40, 20, 3), (20, 10, 3), (10, 5, 3)]
np.random.seed(0)
data = [np.random.random(s) for s in shapes]
layer = Pyramid(data, multichannel=False)
assert layer.data == data
assert layer.ndim == len(shapes[0])
assert layer.shape == shapes[0]
assert layer.multichannel == False
def test_non_uniform_3D_pyramid():
"""Test instantiating Pyramid layer non-uniform 3D data."""
shapes = [(8, 40, 20), (8, 20, 10), (8, 10, 5)]
np.random.seed(0)
data = [np.random.random(s) for s in shapes]
layer = Pyramid(data)
assert layer.data == data
assert layer.ndim == len(shapes[0])
assert layer.shape == shapes[0]
assert layer.multichannel == False
assert layer._data_view.ndim == 2
def test_random_pyramid():
"""Test instantiating Pyramid layer with random 2D data."""
shapes = [(40, 20), (20, 10), (10, 5)]
np.random.seed(0)
data = [np.random.random(s) for s in shapes]
layer = Pyramid(data)
assert layer.data == data
assert layer.ndim == len(shapes[0])
assert layer.shape == shapes[0]
assert layer.multichannel == False
assert layer._data_view.ndim == 2
def test_3D_rgb_pyramid():
"""Test instantiating Pyramid layer with 3D RGB data."""
shapes = [(8, 40, 20, 3), (4, 20, 10, 3), (2, 10, 5, 3)]
np.random.seed(0)
data = [np.random.random(s) for s in shapes]
layer = Pyramid(data)
assert layer.data == data
assert layer.ndim == len(shapes[0]) - 1
assert layer.shape == shapes[0][:-1]
assert layer.multichannel == True
assert layer._data_view.ndim == 3
def test_clims():
"""Test setting color limits."""
shapes = [(40, 20), (20, 10), (10, 5)]
np.random.seed(0)
data = [np.random.random(s) for s in shapes]
layer = Pyramid(data)
assert layer.clim[0] >= 0
assert layer.clim[1] <= 1
assert layer.clim[0] < layer.clim[1]
assert layer.clim == layer._clim_range
# Change clim property
clim = [0, 2]
layer.clim = clim
assert layer.clim == clim
assert layer._clim_range == clim
# Set clim as keyword argument
layer = Pyramid(data, clim=clim)
assert layer.clim == clim
assert layer._clim_range == clim
def test_contrast_limits():
"""Test setting color limits."""
shapes = [(40, 20), (20, 10), (10, 5)]
np.random.seed(0)
data = [np.random.random(s) for s in shapes]
layer = Pyramid(data)
assert layer.contrast_limits[0] >= 0
assert layer.contrast_limits[1] <= 1
assert layer.contrast_limits[0] < layer.contrast_limits[1]
assert layer.contrast_limits == layer._contrast_limits_range
# Change contrast_limits property
contrast_limits = [0, 2]
layer.contrast_limits = contrast_limits
assert layer.contrast_limits == contrast_limits
assert layer._contrast_limits_range == contrast_limits
# Set contrast_limits as keyword argument
layer = Pyramid(data, contrast_limits=contrast_limits)
assert layer.contrast_limits == contrast_limits
assert layer._contrast_limits_range == contrast_limits
def test_visiblity():
"""Test setting layer visiblity."""
shapes = [(40, 20), (20, 10), (10, 5)]
np.random.seed(0)
data = [np.random.random(s) for s in shapes]
layer = Pyramid(data)
assert layer.visible == True
layer.visible = False
assert layer.visible == False
layer = Pyramid(data, visible=False)
assert layer.visible == False
layer.visible = True
assert layer.visible == True
def test_blending():
"""Test setting layer blending."""
shapes = [(40, 20), (20, 10), (10, 5)]
np.random.seed(0)
data = [np.random.random(s) for s in shapes]
layer = Pyramid(data)
assert layer.blending == 'translucent'
layer.blending = 'additive'
assert layer.blending == 'additive'
layer = Pyramid(data, blending='additive')
assert layer.blending == 'additive'
layer.blending = 'opaque'
assert layer.blending == 'opaque'
def test_opacity():
"""Test setting layer opacity."""
shapes = [(40, 20), (20, 10), (10, 5)]
np.random.seed(0)
data = [np.random.random(s) for s in shapes]
layer = Pyramid(data)
assert layer.opacity == 1.0
layer.opacity = 0.5
assert layer.opacity == 0.5
layer = Pyramid(data, opacity=0.6)
assert layer.opacity == 0.6
layer.opacity = 0.3
assert layer.opacity == 0.3
def test_colormaps():
"""Test setting test_colormaps."""
shapes = [(40, 20), (20, 10), (10, 5)]
np.random.seed(0)
data = [np.random.random(s) for s in shapes]
layer = Pyramid(data)
assert layer.colormap[0] == 'gray'
assert type(layer.colormap[1]) == Colormap
layer.colormap = 'magma'
assert layer.colormap[0] == 'magma'
assert type(layer.colormap[1]) == Colormap
cmap = Colormap([[0.0, 0.0, 0.0, 0.0], [0.3, 0.7, 0.2, 1.0]])
layer.colormap = 'custom', cmap
assert layer.colormap[0] == 'custom'
assert layer.colormap[1] == cmap
cmap = Colormap([[0.0, 0.0, 0.0, 0.0], [0.7, 0.2, 0.6, 1.0]])
layer.colormap = {'new': cmap}
assert layer.colormap[0] == 'new'
assert layer.colormap[1] == cmap
layer = Pyramid(data, colormap='magma')
assert layer.colormap[0] == 'magma'
assert type(layer.colormap[1]) == Colormap
cmap = Colormap([[0.0, 0.0, 0.0, 0.0], [0.3, 0.7, 0.2, 1.0]])
layer = Pyramid(data, colormap=('custom', cmap))
assert layer.colormap[0] == 'custom'
assert layer.colormap[1] == cmap
cmap = Colormap([[0.0, 0.0, 0.0, 0.0], [0.7, 0.2, 0.6, 1.0]])
layer = Pyramid(data, colormap={'new': cmap})
assert layer.colormap[0] == 'new'
assert layer.colormap[1] == cmap