def test_value():
"""Test getting the value of the data at the current coordinates."""
np.random.seed(0)
data = np.random.random((10, 15, 20))
layer = Image(data)
layer._slice_dims(ndisplay=3)
value = layer.get_value((0,) * 3)
assert value == data[0, 0, 0]
def test_message():
"""Test converting value and coords to message."""
np.random.seed(0)
data = np.random.random((10, 15, 20))
layer = Image(data)
layer._slice_dims(ndisplay=3)
msg = layer.get_status(layer.position)
assert type(msg) == str
def test_all_zeros_volume():
"""Test instantiating Image layer with all zeros data."""
shape = (10, 15, 20)
data = np.zeros(shape, dtype=float)
layer = Image(data)
layer._slice_dims(ndisplay=3)
assert np.all(layer.data == data)
assert layer.ndim == len(shape)
np.testing.assert_array_equal(layer.extent.data[1] + 1, shape)
assert layer._data_view.shape == shape[-3:]
def test_4D_volume():
"""Test instantiating multiple Image layers with random 4D data."""
shape = (10, 15, 6, 8)
np.random.seed(0)
data = np.random.random(shape)
layer = Image(data)
layer._slice_dims(ndisplay=3)
assert np.all(layer.data == data)
assert layer.ndim == len(shape)
np.testing.assert_array_equal(layer.extent.data[1] + 1, shape)
assert layer._data_view.shape == shape[-3:]
def test_integer_volume():
"""Test instantiating Image layer with integer data."""
shape = (10, 15, 20)
np.random.seed(0)
data = np.round(10 * np.random.random(shape)).astype(int)
layer = Image(data)
layer._slice_dims(ndisplay=3)
assert np.all(layer.data == data)
assert layer.ndim == len(shape)
np.testing.assert_array_equal(layer.extent.data[1] + 1, shape)
assert layer._data_view.shape == shape[-3:]
def test_3D_volume():
"""Test instantiating Image layer with random 3D data."""
shape = (10, 15, 6)
np.random.seed(0)
data = np.random.random(shape)
layer = Image(data)
layer._slice_dims(ndisplay=3)
assert np.all(layer.data == data)
assert layer.ndim == len(shape)
assert layer.shape == shape
assert layer._data_view.shape == shape[-3:]
def test_plane_controls_show_hide_on_ndisplay_change(qtbot):
"""Changing ndisplay should show/hide plane controls if depicting a plane."""
layer = Image(np.random.rand(10, 15, 20))
qtctrl = QtImageControls(layer)
qtbot.addWidget(qtctrl)
layer._slice_dims(ndisplay=3)
layer.depiction = 'plane'
assert not qtctrl.planeControls.isHidden() # isVisible() != not isHidden()
layer._slice_dims(ndisplay=2)
assert qtctrl.planeControls.isHidden()
def test_projected_distance_from_mouse_drag(start_position, end_position,
view_direction, vector,
expected_value):
image = Image(np.ones((32, 32, 32)))
image._slice_dims(point=[0, 0, 0], ndisplay=3)
result = image.projected_distance_from_mouse_drag(
start_position,
end_position,
view_direction,
vector,
dims_displayed=[0, 1, 2],
)
assert np.allclose(result, expected_value)
def test_value_3d(position, view_direction, dims_displayed, world):
"""Currently get_value should return None in 3D"""
np.random.seed(0)
data = np.random.random((10, 15, 15))
layer = Image(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 is None
def test_auto_contrast_buttons(qtbot):
layer = Image(np.arange(8**3).reshape(8, 8, 8), contrast_limits=(0, 1))
qtctrl = QtImageControls(layer)
qtbot.addWidget(qtctrl)
assert layer.contrast_limits == [0, 1]
qtctrl.autoScaleBar._once_btn.click()
assert layer.contrast_limits == [0, 63]
# change slice
layer._slice_dims((1, 8, 8))
# hasn't changed yet
assert layer.contrast_limits == [0, 63]
# with auto_btn, it should always change
qtctrl.autoScaleBar._auto_btn.click()
assert layer.contrast_limits == [64, 127]
layer._slice_dims((2, 8, 8))
assert layer.contrast_limits == [128, 191]
layer._slice_dims((3, 8, 8))
assert layer.contrast_limits == [192, 255]
# once button turns off continuous
qtctrl.autoScaleBar._once_btn.click()
layer._slice_dims((4, 8, 8))
assert layer.contrast_limits == [192, 255]
def test_changing_volume():
"""Test changing Image data."""
shape_a = (10, 15, 30)
shape_b = (20, 12, 6)
np.random.seed(0)
data_a = np.random.random(shape_a)
data_b = np.random.random(shape_b)
layer = Image(data_a)
layer._slice_dims(ndisplay=3)
layer.data = data_b
assert np.all(layer.data == data_b)
assert layer.ndim == len(shape_b)
np.testing.assert_array_equal(layer.extent.data[1] + 1, shape_b)
assert layer._data_view.shape == shape_b[-3:]
def test_scale():
"""Test instantiating anisotropic 3D volume."""
shape = (10, 15, 20)
scale = [3, 1, 1]
full_shape = tuple(np.multiply(shape, scale))
np.random.seed(0)
data = np.random.random(shape)
layer = Image(data, scale=scale)
layer._slice_dims(ndisplay=3)
assert np.all(layer.data == data)
assert layer.ndim == len(shape)
assert layer.shape == full_shape
# Note that the scale appears as the step size in the range
assert layer._data_view.shape == shape[-3:]
def test_depiction_combobox_changes(qtbot):
"""Changing the model attribute should update the view."""
layer = Image(np.random.rand(10, 15, 20))
layer._slice_dims(ndisplay=3)
qtctrl = QtImageControls(layer)
qtbot.addWidget(qtctrl)
combo_box = qtctrl.depictionComboBox
opts = {combo_box.itemText(i) for i in range(combo_box.count())}
depiction_options = {
'volume',
'plane',
}
assert opts == depiction_options
layer.depiction = 'plane'
assert combo_box.findText('plane') == combo_box.currentIndex()
layer.depiction = 'volume'
assert combo_box.findText('volume') == combo_box.currentIndex()
def test_scale():
"""Test instantiating anisotropic 3D volume."""
shape = (10, 15, 20)
scale = [3, 1, 1]
full_shape = tuple(np.multiply(shape, scale))
np.random.seed(0)
data = np.random.random(shape)
layer = Image(data, scale=scale)
layer._slice_dims(ndisplay=3)
assert np.all(layer.data == data)
assert layer.ndim == len(shape)
np.testing.assert_array_equal(
layer.extent.world[1] - layer.extent.world[0], full_shape)
pixel_extent_end = np.asarray(full_shape) - 0.5 * np.asarray(scale)
np.testing.assert_array_equal(layer.extent.world[1], pixel_extent_end)
# Note that the scale appears as the step size in the range
assert layer._data_view.shape == shape[-3:]
def test_plane_controls_show_hide_on_ndisplay_change(qtbot):
"""Changing ndisplay should show/hide plane controls if depicting a plane."""
layer = Image(np.random.rand(10, 15, 20))
qtctrl = QtImageControls(layer)
qtbot.addWidget(qtctrl)
layer._slice_dims(ndisplay=3)
layer.depiction = 'plane'
assert not qtctrl.planeThicknessSlider.isHidden()
assert not qtctrl.planeThicknessLabel.isHidden()
assert not qtctrl.planeNormalButtons.isHidden()
assert not qtctrl.planeNormalLabel.isHidden()
layer._slice_dims(ndisplay=2)
assert qtctrl.planeThicknessSlider.isHidden()
assert qtctrl.planeThicknessLabel.isHidden()
assert qtctrl.planeNormalButtons.isHidden()
assert qtctrl.planeNormalLabel.isHidden()
def test_switching_displayed_dimensions():
"""Test instantiating data then switching to displayed."""
shape = (10, 15, 20)
np.random.seed(0)
data = np.random.random(shape)
layer = Image(data)
assert np.all(layer.data == data)
assert layer.ndim == len(shape)
np.testing.assert_array_equal(layer.extent.data[1] + 1, shape)
# check displayed data is initially 2D
assert layer._data_view.shape == shape[-2:]
layer._slice_dims(ndisplay=3)
# check displayed data is now 3D
assert layer._data_view.shape == shape[-3:]
layer._slice_dims(ndisplay=2)
# check displayed data is now 2D
assert layer._data_view.shape == shape[-2:]
layer = Image(data)
layer._slice_dims(ndisplay=3)
assert np.all(layer.data == data)
assert layer.ndim == len(shape)
np.testing.assert_array_equal(layer.extent.data[1] + 1, shape)
# check displayed data is initially 3D
assert layer._data_view.shape == shape[-3:]
layer._slice_dims(ndisplay=2)
# check displayed data is now 2D
assert layer._data_view.shape == shape[-2:]
layer._slice_dims(ndisplay=3)
# check displayed data is now 3D
assert layer._data_view.shape == shape[-3:]
