def test_nD_volume_launch(qtbot):
"""Test adding nD volume when viewer launched with 3D."""
viewer = Viewer(ndisplay=3)
view = viewer.window.qt_viewer
qtbot.addWidget(view)
np.random.seed(0)
shape = (6, 10, 15, 20)
data = np.random.random(shape)
viewer.add_image(data)
assert np.all(viewer.layers[0].data == data)
assert viewer.layers[0]._data_view.shape == shape[-3:]
assert len(viewer.layers) == 1
assert view.layers.vbox_layout.count() == 2 * len(viewer.layers) + 2
assert viewer.dims.ndim == 4
assert view.dims.nsliders == viewer.dims.ndim
assert np.sum(view.dims._displayed_sliders) == 1
# Switch to 3D rendering
assert viewer.dims.ndisplay == 3
viewer.dims.ndisplay = 2
assert viewer.dims.ndisplay == 2
# Close the viewer
viewer.window.close()
def test_nD_shapes(qtbot):
"""Test adding vectors."""
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
np.random.seed(0)
# create one random rectangle per "plane"
planes = np.tile(np.arange(10).reshape((10, 1, 1)), (1, 4, 1))
corners = np.random.uniform(0, 10, size=(10, 4, 2))
data = np.concatenate((planes, corners), axis=2)
viewer.add_shapes(data)
assert np.all(
[np.all(ld == d) for ld, d in zip(viewer.layers[0].data, data)]
)
assert len(viewer.layers) == 1
assert view.layers.vbox_layout.count() == 2 * len(viewer.layers) + 2
assert viewer.dims.ndim == 3
assert view.dims.nsliders == viewer.dims.ndim
assert np.sum(view.dims._displayed_sliders) == 1
# Flip dims order displayed
viewer.dims.order = [0, 2, 1]
assert viewer.dims.order == [0, 2, 1]
# Flip dims order including non-displayed
viewer.dims.order = [1, 0, 2]
assert viewer.dims.order == [1, 0, 2]
# Close the viewer
viewer.window.close()
def test_nD_image(qtbot):
"""Test adding nD image."""
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
np.random.seed(0)
data = np.random.random((6, 10, 15))
viewer.add_image(data)
assert np.all(viewer.layers[0].data == data)
assert len(viewer.layers) == 1
assert view.layers.vbox_layout.count() == 2 * len(viewer.layers) + 2
assert viewer.dims.ndim == 3
assert view.dims.nsliders == viewer.dims.ndim
assert np.sum(view.dims._displayed_sliders) == 1
# Flip dims order displayed
viewer.dims.order = [0, 2, 1]
assert viewer.dims.order == [0, 2, 1]
# Flip dims order including non-displayed
viewer.dims.order = [1, 0, 2]
assert viewer.dims.order == [1, 0, 2]
# Switch to 3D rendering
viewer.dims.ndisplay = 3
assert np.sum(view.dims._displayed_sliders) == 0
assert viewer.dims.ndisplay == 3
viewer.dims.ndisplay = 2
assert viewer.dims.ndisplay == 2
# Close the viewer
viewer.window.close()
def test_nD_volume_launch_order(qtbot):
"""Test adding nD volume when viewer launched with 3D."""
order = [1, 0, 2, 3]
viewer = Viewer(ndisplay=3, order=order)
view = viewer.window.qt_viewer
qtbot.addWidget(view)
np.random.seed(0)
shape = (6, 10, 15, 20)
data = np.random.random(shape)
viewer.add_image(data)
assert np.all(viewer.layers[0].data == data)
assert viewer.layers[0]._data_view.shape == tuple(
shape[o] for o in order[-3:]
)
assert len(viewer.layers) == 1
assert view.layers.vbox_layout.count() == 2 * len(viewer.layers) + 2
assert viewer.dims.ndim == 4
assert view.dims.nsliders == viewer.dims.ndim
assert np.sum(view.dims._displayed_sliders) == 1
assert viewer.dims.order == order
# Close the viewer
viewer.window.close()
def test_add_surface(qtbot):
"""Test adding 3D surface."""
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
np.random.seed(0)
vertices = np.random.random((10, 3))
faces = np.random.randint(10, size=(6, 3))
values = np.random.random(10)
data = (vertices, faces, values)
layer = viewer.add_surface(data)
assert np.all(
[np.all(vd == d) for vd, d in zip(viewer.layers[0].data, data)])
assert len(viewer.layers) == 1
assert view.layers.vbox_layout.count() == 2 * len(viewer.layers) + 2
assert viewer.dims.ndim == 3
assert view.dims.nsliders == viewer.dims.ndim
assert np.sum(view.dims._displayed_sliders) == 1
# Switch to 3D rendering mode and back to 2D rendering mode
viewer.dims.ndisplay = 3
assert viewer.dims.ndisplay == 3
viewer.dims.ndisplay = 2
assert viewer.dims.ndisplay == 2
# Run all class keybindings
for func in layer.class_keymap.values():
func(layer)
# Close the viewer
viewer.window.close()
def test_nD_vectors(qtbot):
"""Test adding nD vectors."""
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
np.random.seed(0)
data = 20 * np.random.random((10, 2, 3))
viewer.add_vectors(data)
assert np.all(viewer.layers[0].data == data)
assert len(viewer.layers) == 1
assert view.layers.vbox_layout.count() == 2 * len(viewer.layers) + 2
assert viewer.dims.ndim == 3
assert view.dims.nsliders == viewer.dims.ndim
assert np.sum(view.dims._displayed_sliders) == 1
# Flip dims order displayed
viewer.dims.order = [0, 2, 1]
assert viewer.dims.order == [0, 2, 1]
# Flip dims order including non-displayed
viewer.dims.order = [1, 0, 2]
assert viewer.dims.order == [1, 0, 2]
# Close the viewer
viewer.window.close()
def test_add_volume(qtbot):
"""Test adding volume."""
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
np.random.seed(0)
data = np.random.random((10, 15, 20))
layer = viewer.add_image(data)
viewer.dims.ndisplay = 3
assert np.all(viewer.layers[0].data == data)
assert len(viewer.layers) == 1
assert view.layers.vbox_layout.count() == 2 * len(viewer.layers) + 2
assert viewer.dims.ndim == 3
assert view.dims.nsliders == viewer.dims.ndim
assert np.sum(view.dims._displayed_sliders) == 0
# Switch to 3D rendering mode and back to 2D rendering mode
viewer.dims.ndisplay = 3
assert viewer.dims.ndisplay == 3
viewer.dims.ndisplay = 2
assert viewer.dims.ndisplay == 2
# Run all class keybindings
for func in layer.class_keymap.values():
func(layer)
# Close the viewer
viewer.window.close()
def test_add_pyramid(qtbot):
"""Test adding image pyramid."""
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
shapes = [(40, 20), (20, 10), (10, 5)]
np.random.seed(0)
data = [np.random.random(s) for s in shapes]
layer = viewer.add_image(data, is_pyramid=True)
assert np.all(viewer.layers[0].data == data)
assert len(viewer.layers) == 1
assert view.layers.vbox_layout.count() == 2 * len(viewer.layers) + 2
assert viewer.dims.ndim == 2
assert view.dims.nsliders == viewer.dims.ndim
assert np.sum(view.dims._displayed_sliders) == 0
# Switch to 3D rendering mode and back to 2D rendering mode
viewer.dims.ndisplay = 3
assert viewer.dims.ndisplay == 3
viewer.dims.ndisplay = 2
assert viewer.dims.ndisplay == 2
# Run all class keybindings
for func in layer.class_keymap.values():
func(layer)
# Close the viewer
viewer.window.close()
def test_image_rendering(qtbot):
"""Test 3D image with different rendering."""
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
data = np.random.random((20, 20, 20))
layer = viewer.add_image(data)
assert layer.rendering == 'mip'
# Change rendering property
layer.rendering = 'translucent'
assert layer.rendering == 'translucent'
# Change rendering property
layer.rendering = 'attenuated_mip'
assert layer.rendering == 'attenuated_mip'
layer.attenuation = 0.2
assert layer.attenuation == 0.2
# Change rendering property
layer.rendering = 'iso'
assert layer.rendering == 'iso'
layer.iso_threshold = 0.3
assert layer.iso_threshold == 0.3
# Change rendering property
layer.rendering = 'additive'
assert layer.rendering == 'additive'
# Close the viewer
viewer.window.close()
def test_update(qtbot):
import time
data = np.random.random((512, 512))
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
layer = viewer.add_image(data)
def layer_update(*, update_period, num_updates):
# number of times to update
for k in range(num_updates):
time.sleep(update_period)
dat = np.random.random((512, 512))
layer.data = dat
assert layer.data.all() == dat.all()
viewer.update(layer_update, update_period=0.01, num_updates=100)
# if we do not sleep, main thread closes before update thread finishes and many qt components get cleaned
time.sleep(3)
# Close the viewer
viewer.window.close()
def __init__(
self,
viewer: Viewer,
im_shape: tuple,
cell_masks: list = [],
initial_state: Union[str, np.ndarray] = "good",
selection_layer_name: str = 'selected_cell',
accepted_layer_name: str = 'accepted_mask',
rejected_layer_name: str = 'rejected_mask',
mode: str = 'all',
):
self.selected_shapes = viewer.add_shapes(name=selection_layer_name)
self.initialize_masks(
viewer=viewer,
im_shape=im_shape,
cell_masks=cell_masks,
initial_state=initial_state,
accepted_layer_name=accepted_layer_name,
rejected_layer_name=rejected_layer_name,
)
viewer.bind_key("t", self.toggle_selected_mask)
self._mode = mode
def test_5D_image_3D_rendering(qtbot):
"""Test 3D rendering of a 5D image."""
np.random.seed(0)
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
# add 4D image data
data = np.random.random((2, 10, 12, 13, 14))
viewer.add_image(data)
assert np.all(viewer.layers[0].data == data)
assert len(viewer.layers) == 1
assert viewer.dims.ndim == 5
assert viewer.dims.ndisplay == 2
assert viewer.layers[0]._data_view.ndim == 2
assert view.dims.nsliders == viewer.dims.ndim
assert np.sum(view.dims._displayed_sliders) == 3
# switch to 3D rendering
viewer.dims.ndisplay = 3
assert viewer.dims.ndisplay == 3
assert viewer.layers[0]._data_view.ndim == 3
assert np.sum(view.dims._displayed_sliders) == 2
# Close the viewer
viewer.window.close()
def test_add_image(qtbot):
"""Test adding image."""
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
np.random.seed(0)
data = np.random.random((10, 15))
viewer.add_image(data)
assert np.all(viewer.layers[0].data == data)
assert len(viewer.layers) == 1
assert view.layers.vbox_layout.count() == 2 * len(viewer.layers) + 2
assert viewer.dims.ndim == 2
assert view.dims.nsliders == viewer.dims.ndim
assert np.sum(view.dims._displayed_sliders) == 0
# Switch to 3D rendering mode and back to 2D rendering mode
viewer.dims.ndisplay = 3
assert viewer.dims.ndisplay == 3
viewer.dims.ndisplay = 2
assert viewer.dims.ndisplay == 2
# Close the viewer
viewer.window.close()
def test_data_change_ndisplay_surface(qtbot):
"""Test change data calls for surface layer with ndisplay change."""
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
np.random.seed(0)
vertices = np.random.random((10, 3))
faces = np.random.randint(10, size=(6, 3))
values = np.random.random(10)
data = (vertices, faces, values)
layer = viewer.add_surface(data)
visual = view.layer_to_visual[layer]
@patch.object(visual, '_on_data_change', wraps=visual._on_data_change)
def test_ndisplay_change(mocked_method, ndisplay=3):
viewer.dims.ndisplay = ndisplay
mocked_method.assert_called_once()
# Switch to 3D rendering mode and back to 2D rendering mode
test_ndisplay_change(ndisplay=3)
test_ndisplay_change(ndisplay=2)
# Close the viewer
viewer.window.close()
def test_nD_pyramid(qtbot):
"""Test adding nD image pyramid."""
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
shapes = [(8, 40, 20), (4, 20, 10), (4, 10, 5)]
np.random.seed(0)
data = [np.random.random(s) for s in shapes]
viewer.add_pyramid(data)
assert np.all(viewer.layers[0].data == data)
assert len(viewer.layers) == 1
assert view.layers.vbox_layout.count() == 2 * len(viewer.layers) + 2
assert viewer.dims.ndim == 3
assert view.dims.nsliders == viewer.dims.ndim
assert np.sum(view.dims._displayed_sliders) == 1
# Flip dims order displayed
viewer.dims.order = [0, 2, 1]
assert viewer.dims.order == [0, 2, 1]
# Flip dims order including non-displayed
viewer.dims.order = [1, 0, 2]
assert viewer.dims.order == [1, 0, 2]
# Close the viewer
viewer.window.close()
def show_ax_dend(v: napari.Viewer, ax: pd.DataFrame, dend: pd.DataFrame,
name: str):
for (data, meta) in zip([ax, dend], metadata):
v.add_points(
data.loc[::10, "x":"z"],
edge_width=0,
name=f"{name}_{meta[1]}",
face_color=f"{meta[0]}",
size=data.loc[::10, 'alpha'],
opacity=0.2,
)
def test_dask_2D(qtbot):
"""Test adding 2D dask image."""
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
da.random.seed(0)
data = da.random.random((10, 15))
viewer.add_image(data)
assert np.all(viewer.layers[0].data == data)
# Close the viewer
viewer.window.close()
def main_window(qtbot, request):
if request.param == "remote":
server.try_kill_server()
viewer = Viewer(show=False)
win = MainWindow(viewer=viewer, remote=request.param == "remote")
config_path = os.path.dirname(os.path.abspath(__file__)) + "/test_config.cfg"
win._mmc.loadSystemConfiguration(config_path)
try:
yield win
finally:
viewer.close()
def test_image_dytpes(qtbot, dtype):
"""Test different dtype images."""
np.random.seed(0)
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
# add dtype image data
data = np.random.randint(20, size=(30, 40)).astype(dtype)
viewer.add_image(data)
assert np.all(viewer.layers[0].data == data)
# Close the viewer
viewer.window.close()
def test_zarr_dask_nD(qtbot):
"""Test adding nD zarr image."""
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
data = zarr.zeros((200, 100, 50), chunks=(40, 20, 10))
data[53:63, 10:20, :] = 1
zdata = da.from_zarr(data)
viewer.add_image(zdata)
assert np.all(viewer.layers[0].data == zdata)
# Close the viewer
viewer.window.close()
def test_zarr_nD(qtbot):
"""Test adding nD zarr image."""
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
data = zarr.zeros((200, 100, 50), chunks=(40, 20, 10))
data[53:63, 10:20, :] = 1
# If passing a zarr file directly, must pass contrast_limits
viewer.add_image(data, contrast_limits=[0, 1])
assert np.all(viewer.layers[0].data == data)
# Close the viewer
viewer.window.close()
def test_xarray_nD(qtbot):
"""Test adding nD xarray image."""
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
np.random.seed(0)
data = np.random.random((10, 15, 6, 16))
xdata = xr.DataArray(data, dims=['t', 'z', 'y', 'x'])
viewer.add_image(xdata)
assert np.all(viewer.layers[0].data == xdata)
# Close the viewer
viewer.window.close()
def __init__(
self,
image: np.ndarray,
viewer: Viewer,
nbins: int = 20,
xlabel: str = '',
ylabel: str = '',
image_layer_name: str = 'image',
name: str = 'histogram',
):
self.image = image
self.image_layer = viewer.add_image(image,
name=image_layer_name,
visible=False)
# create the histogram
self.nbins = nbins
counts, values = self._calculate_histogram()
self.histogram_widget = HistogramWidget(values,
counts,
xlabel=xlabel,
ylabel=ylabel)
self._threshold = 0
# update the SNR image and connect the event
self.on_snr_changed()
self.histogram_widget.threshold_changed_callbacks.append(
self.on_snr_changed)
# add the histogram dock widget to the viewer
viewer.window.add_dock_widget(self.histogram_widget, name=name)
def show_pairs(viewer: napari.Viewer, data: pd.DataFrame):
"""Highlights interesting pairs from the axonal and dendritic trees."""
viewer.add_points(
data.loc[:, 'ax_x':'ax_z'],
edge_width=0,
name='ax',
face_color='green',
size=data.loc[:, 'ax_alpha'],
)
viewer.add_points(
data.loc[:, 'dend_x':'dend_z'],
edge_width=0,
name='dend',
face_color='orange',
size=data.loc[:, 'dend_alpha'],
)
def test_viewer(qtbot):
"""Test instantiating viewer."""
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
assert viewer.title == 'napari'
assert view.viewer == viewer
assert len(viewer.layers) == 0
assert view.layers.vbox_layout.count() == 2
assert viewer.dims.ndim == 2
assert view.dims.nsliders == viewer.dims.ndim
assert np.sum(view.dims._displayed_sliders) == 0
# Switch to 3D rendering mode and back to 2D rendering mode
viewer.dims.ndisplay = 3
assert viewer.dims.ndisplay == 3
viewer.dims.ndisplay = 2
assert viewer.dims.ndisplay == 2
# Run all class keybindings
for func in viewer.class_keymap.values():
func(viewer)
# the `play` keybinding calls QtDims.play_dim(), which then creates a new QThread.
# we must then run the keybinding a second time, which will call QtDims.stop(),
# otherwise the thread will be killed at the end of the test without cleanup,
# causing a segmentation fault. (though the tests still pass)
if func.__name__ == 'play':
func(viewer)
# Close the viewer
viewer.window.close()
def test_viewer(qtbot):
"""Test instantiating viewer."""
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
assert viewer.title == 'napari'
assert view.viewer == viewer
assert len(viewer.layers) == 0
assert view.layers.vbox_layout.count() == 2
assert viewer.dims.ndim == 2
assert view.dims.nsliders == viewer.dims.ndim
assert np.sum(view.dims._displayed_sliders) == 0
# Switch to 3D rendering mode and back to 2D rendering mode
viewer.dims.ndisplay = 3
assert viewer.dims.ndisplay == 3
viewer.dims.ndisplay = 2
assert viewer.dims.ndisplay == 2
# Run all class keybindings
for func in viewer.class_keymap.values():
func(viewer)
# Close the viewer
viewer.window.close()
def _run_plugin_module(mod, plugin_name):
"""Register `mod` as a plugin, find/create viewer, and run napari."""
from napari.plugins import plugin_manager
plugin_manager.register(mod, name=plugin_name)
# now, check if a viewer was created, and if not, create one.
for obj in mod.values():
if isinstance(obj, Viewer):
_v = obj
break
else:
_v = Viewer()
try:
_v.window._qt_window.parent()
except RuntimeError:
# this script had a napari.run() in it, and the viewer has already been
# used and cleaned up... if we eventually have "reusable viewers", we
# can continue here
return
# finally, if the file declared a dock widget, add it to the viewer.
dws = plugin_manager.hooks.napari_experimental_provide_dock_widget
if any(i.plugin_name == plugin_name for i in dws.get_hookimpls()):
_v.window.add_plugin_dock_widget(plugin_name)
run()
def actual_factory(*model_args, **model_kwargs):
model_kwargs['show'] = model_kwargs.pop(
'show', request.config.getoption("--show-viewer")
)
viewer = Viewer(*model_args, **model_kwargs)
viewers.append(viewer)
return viewer
def main():
with gui_qt():
viewer = Viewer()
m = OMEROWidget()
dw = viewer.window.add_dock_widget(m, area="right")
# TODO: figure out dynamic geometry
viewer.window._qt_window.setGeometry(300, 200, 1280, 720)
viewer.window._qt_window.resizeDocks([dw], [390], Qt.Horizontal)
def test_pyramid_dytpes(qtbot, dtype):
"""Test different dtype pyramids."""
np.random.seed(0)
viewer = Viewer()
view = viewer.window.qt_viewer
qtbot.addWidget(view)
# add dtype pyramid data
data = [
np.random.randint(20, size=(30, 40)).astype(dtype),
np.random.randint(20, size=(15, 20)).astype(dtype),
]
viewer.add_pyramid(data)
assert np.all(viewer.layers[0].data == data)
# Close the viewer
viewer.window.close()
