def test_viewer_open_no_plugin(tmp_path):
viewer = ViewerModel()
fname = tmp_path / 'gibberish.gbrsh'
fname.touch()
with pytest.raises(ValueError, match='No plugin found capable of reading'):
# will default to builtins
viewer.open(fname)
def test_viewer_open_no_plugin(tmp_path):
viewer = ViewerModel()
fname = tmp_path / 'gibberish.gbrsh'
fname.touch()
with pytest.raises(ValueError) as e:
viewer.open(fname)
assert 'No plugin found capable of reading' in str(e.value)
def test_dask_2D():
"""Test adding 2D dask image."""
viewer = ViewerModel()
da.random.seed(0)
data = da.random.random((10, 15))
viewer.add_image(data)
assert np.all(viewer.layers[0].data == data)
def test_viewer_open_no_plugin(tmp_path):
viewer = ViewerModel()
fname = tmp_path / 'gibberish.gbrsh'
fname.touch()
with pytest.raises(ValueError) as e:
# will default to builtins
viewer.open(fname)
assert "Plugin 'builtins' does not support file(s)" in str(e.value)
def test_xarray_nD():
"""Test adding nD xarray image."""
viewer = ViewerModel()
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)
def test_zarr_nD():
"""Test adding nD zarr image."""
viewer = ViewerModel()
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)
def test_zarr_dask_nD():
"""Test adding nD zarr image."""
viewer = ViewerModel()
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)
def test_add_layers_with_plugins(layer_datum):
"""Test that add_layers_with_plugins adds the expected layer types."""
with patch(
"napari.components.add_layers_mixin.read_data_with_plugins",
MagicMock(return_value=[layer_datum]),
):
v = ViewerModel()
v._add_layers_with_plugins('mock_path')
layertypes = [l._type_string for l in v.layers]
assert layertypes == [layer_datum[2]]
def test_add_layers_with_plugins(layer_datum):
"""Test that add_layers_with_plugins adds the expected layer types."""
with patch(
"napari.plugins.io.read_data_with_plugins",
MagicMock(return_value=([layer_datum], _testimpl)),
):
v = ViewerModel()
v._add_layers_with_plugins('mock_path')
layertypes = [layer._type_string for layer in v.layers]
assert layertypes == [layer_datum[2]]
expected_source = Source(path='mock_path', reader_plugin='testimpl')
assert all(lay.source == expected_source for lay in v.layers)
def test_add_layers_with_plugins_and_kwargs(layer_data, kwargs):
"""Test that _add_layers_with_plugins kwargs override plugin kwargs.
see also: napari.components._test.test_prune_kwargs
"""
with patch(
"napari.components.add_layers_mixin.read_data_with_plugins",
MagicMock(return_value=layer_data),
):
v = ViewerModel()
v._add_layers_with_plugins('mock_path', kwargs=kwargs)
for layer in v.layers:
for key, val in kwargs.items():
assert getattr(layer, key) == val
def test_receive_return_proxy_object():
"""Test that an"""
viewer = ViewerModel()
viewer.add_image(np.random.random((20, 20)))
pv = PublicOnlyProxy(viewer)
# simulates behavior from outside of napari
with patch('napari.utils.misc.ROOT_DIR', new='/some/other/package'):
# the recursion means this layer will be a Proxy Object on __getitem__
layer = pv.layers[-1]
assert isinstance(layer, PublicOnlyProxy)
# remove and add it back, should be fine
add_layer = getattr(pv, 'add_layer')
add_layer(layer)
assert len(viewer.layers) == 2
def test_dims_sorter_with_reordered_init(qtbot):
viewer = ViewerModel()
viewer.dims.order = (1, 0)
dim_sorter = QtDimsSorter(viewer)
qtbot.addWidget(dim_sorter)
assert tuple(dim_sorter.axes_list) == tuple(viewer.dims.order)
def test_add_layers_with_plugins_and_kwargs(layer_data, kwargs):
"""Test that _add_layers_with_plugins kwargs override plugin kwargs.
see also: napari.components._test.test_prune_kwargs
"""
with patch(
"napari.components.add_layers_mixin.read_data_with_plugins",
MagicMock(return_value=layer_data),
):
v = ViewerModel()
v._add_layers_with_plugins('mock_path', kwargs=kwargs)
for layer in v.layers:
for key, val in kwargs.items():
assert getattr(layer, key) == val
# if plugins don't provide "name", it falls back to path name
if 'name' not in kwargs:
assert layer.name.startswith('mock_path')
def test_add_layers_with_plugins_and_kwargs(layer_data, kwargs):
"""Test that _add_layers_with_plugins kwargs override plugin kwargs.
see also: napari.components._test.test_prune_kwargs
"""
with patch(
"napari.plugins.io.read_data_with_plugins",
MagicMock(return_value=(layer_data, _testimpl)),
):
v = ViewerModel()
v._add_layers_with_plugins(['mock_path'], kwargs=kwargs, stack=False)
expected_source = Source(path='mock_path', reader_plugin='testimpl')
for layer in v.layers:
for key, val in kwargs.items():
assert getattr(layer, key) == val
# if plugins don't provide "name", it falls back to path name
if 'name' not in kwargs:
assert layer.name.startswith('mock_path')
assert layer.source == expected_source
def test_dims_sorter(qtbot):
viewer = ViewerModel()
dim_sorter = QtDimsSorter(viewer)
qtbot.addWidget(dim_sorter)
assert tuple(dim_sorter.axes_list) == (0, 1)
viewer.dims.axis_labels = ('y', 'x')
assert tuple(dim_sorter.axes_list) == ('y', 'x')
dim_sorter.axes_list.move(1, 0)
assert tuple(dim_sorter.axes_list) == ('x', 'y')
assert tuple(viewer.dims.order) == (1, 0)
def test_viewer_open():
"""Test that a plugin to returning nothing adds nothing to the Viewer."""
viewer = ViewerModel()
assert len(viewer.layers) == 0
viewer.open('mock_path')
assert len(viewer.layers) == 1
viewer.open('mock_path', stack=True)
assert len(viewer.layers) == 2
def test_viewer_open():
"""Test that a plugin to returning an image adds stuff to the viewer."""
viewer = ViewerModel()
assert len(viewer.layers) == 0
viewer.open('mock_path.tif')
assert len(viewer.layers) == 1
# The name should be taken from the path name, stripped of extension
assert viewer.layers[0].name == 'mock_path'
# stack=True also works... and very long names are truncated
viewer.open('mock_path.tif', stack=True)
assert len(viewer.layers) == 2
assert viewer.layers[1].name.startswith('mock_path')
def test_image_dytpes(dtype):
"""Test different dtype images."""
np.random.seed(0)
viewer = ViewerModel()
# 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)
# add dtype multiscale data
data = [
np.random.randint(20, size=(30, 40)).astype(dtype),
np.random.randint(20, size=(15, 20)).astype(dtype),
]
viewer.add_image(data, multiscale=True)
assert np.all(viewer.layers[1].data == data)
def test_viewer_method():
viewer = PublicOnlyProxy(ViewerModel())
assert viewer.add_points() is not None
def test_public_proxy_limited_to_napari(patched_root_dir):
"""Test that the recursive public proxy goes no farther than napari."""
viewer = ViewerModel()
viewer.add_points(None)
pv = PublicOnlyProxy(viewer)
assert not isinstance(pv.layers[0].data, PublicOnlyProxy)
def test_array_from_proxy_objects(patched_root_dir):
"""Test that the recursive public proxy goes no farther than napari."""
viewer = ViewerModel()
viewer.add_points(None)
pv = PublicOnlyProxy(viewer)
assert isinstance(np.array(pv.dims.displayed, dtype=int), np.ndarray)
def test_plugin_returns_nothing():
"""Test that a plugin to returning nothing adds nothing to the Viewer."""
v = ViewerModel()
v._add_layers_with_plugins('mock_path')
assert not v.layers