def test_sample_hook(builtins, tmp_plugin: DynamicPlugin):
viewer = ViewerModel()
NAME = tmp_plugin.name
KEY = 'random data'
with pytest.raises(KeyError, match=f"Plugin {NAME!r} does not provide"):
viewer.open_sample(NAME, KEY)
@tmp_plugin.contribute.sample_data(key=KEY)
def _generate_random_data(shape=(512, 512)):
data = np.random.rand(*shape)
return [(data, {'name': KEY})]
LOGO = str(Path(napari.__file__).parent / 'resources' / 'logo.png')
tmp_plugin.manifest.contributions.sample_data.append(
SampleDataURI(uri=LOGO, key='napari logo', display_name='Napari logo')
)
assert len(viewer.layers) == 0
viewer.open_sample(NAME, KEY)
assert viewer.layers[-1].source == Source(
path=None, reader_plugin=None, sample=(NAME, KEY)
)
assert len(viewer.layers) == 1
viewer.open_sample(NAME, 'napari logo')
assert viewer.layers[-1].source == Source(
path=LOGO, reader_plugin='napari', sample=(NAME, 'napari logo')
)
# test calling with kwargs
viewer.open_sample(NAME, KEY, shape=(256, 256))
assert len(viewer.layers) == 3
assert viewer.layers[-1].source == Source(sample=(NAME, KEY))
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_get_channel_data_from_layer_source(self, mock_aics_image):
# Arrange
data = numpy.ones((75, 100, 100))
mock_image = create_autospec(AICSImage)
mock_aics_image.return_value = mock_image
img_path = "/path/to/image.tiff"
layer = MockLayer(name="Test", source=Source(path=img_path, reader_plugin="builtins"))
mock_image.get_image_data.return_value = data
# Act
result = self._layer_reader.get_channel_data(1, layer)
# Assert
assert numpy.array_equal(result, data)
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')
expected_source = Source(path='mock_path.tif', reader_plugin='testimpl')
assert all(lay.source == expected_source for lay in viewer.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.plugins.io.read_data_with_plugins",
MagicMock(return_value=(layer_data, _testimpl)),
):
v = ViewerModel()
v._add_layers_with_plugins('mock_path', kwargs=kwargs)
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_get_channels_from_layer_source(self, mock_aics_image: Mock):
# Arrange
mock_image = create_autospec(AICSImage)
mock_aics_image.return_value = mock_image
img_path = "/path/to/image.tiff"
layer = MockLayer(name="Test", source=Source(path=img_path, reader_plugin="builtins"))
mock_channels = Mock(return_value=["Test1", "Test2", "Test3"])
mock_image.channel_names = mock_channels.return_value
# Act
channels = self._layer_reader.get_channels(layer)
# Assert
assert channels is not None
assert len(channels) == 3
assert "Test1" == channels[0].name
assert "Test2" == channels[1].name
assert "Test3" == channels[2].name
mock_aics_image.assert_called_with(img_path)
def test_source_context():
"""Test nested contexts, overrides, and resets."""
assert current_source() == Source()
# everything created within this context will have this sample source
with layer_source(sample=('samp', 'name')):
assert current_source() == Source(sample=('samp', 'name'))
# nested contexts override previous ones
with layer_source(path='a', reader_plugin='plug'):
assert current_source() == Source(path='a',
reader_plugin='plug',
sample=('samp', 'name'))
# note the new path now...
with layer_source(path='b'):
assert current_source() == Source(path='b',
reader_plugin='plug',
sample=('samp', 'name'))
# as we exit the contexts, they should undo their assignments
assert current_source() == Source(path='a',
reader_plugin='plug',
sample=('samp', 'name'))
assert current_source() == Source(sample=('samp', 'name'))
assert current_source() == Source()
def test_sample_hook(test_plugin_manager, monkeypatch):
viewer = ViewerModel()
test_plugin_manager.project_name = 'napari'
test_plugin_manager.add_hookspecs(plugins.hook_specifications)
hook = test_plugin_manager.hook.napari_provide_sample_data
hook.call_historic(
result_callback=plugins.register_sample_data, with_impl=True
)
registered = {}
monkeypatch.setattr(plugins, "_sample_data", registered)
with pytest.raises(KeyError) as e:
viewer.open_sample('test_plugin', 'random data')
assert (
"Plugin 'test_plugin' does not provide sample data named 'random data'"
in str(e)
)
def _generate_random_data(shape=(512, 512)):
data = np.random.rand(*shape)
return [(data, {'name': 'random data'})]
LOGO = Path(napari.__file__).parent / 'resources' / 'logo.png'
class test_plugin:
@napari_hook_implementation
def napari_provide_sample_data():
return {
'random data': _generate_random_data,
'napari logo': LOGO,
'samp_key': {
'data': _generate_random_data,
'display_name': 'I look gorgeous in the menu!',
},
}
test_plugin_manager.register(test_plugin)
reg = registered['test_plugin']
assert reg['random data']['data'] == _generate_random_data
assert reg['random data']['display_name'] == 'random data'
assert reg['napari logo']['data'] == LOGO
assert reg['napari logo']['display_name'] == 'napari logo'
assert reg['samp_key']['data'] == _generate_random_data
assert reg['samp_key']['display_name'] == 'I look gorgeous in the menu!'
assert len(viewer.layers) == 0
viewer.open_sample('test_plugin', 'random data')
assert viewer.layers[-1].source == Source(
path=None, reader_plugin=None, sample=('test_plugin', 'random data')
)
assert len(viewer.layers) == 1
viewer.open_sample('test_plugin', 'napari logo')
assert viewer.layers[-1].source == Source(
path=str(LOGO),
reader_plugin='builtins',
sample=('test_plugin', 'napari logo'),
)
assert len(viewer.layers) == 2
viewer.open_sample('test_plugin', 'samp_key')
assert viewer.layers[-1].source == Source(
sample=('test_plugin', 'samp_key')
)
assert len(viewer.layers) == 3
# test calling with kwargs
viewer.open_sample('test_plugin', 'samp_key', shape=(256, 256))
assert len(viewer.layers) == 4
assert viewer.layers[-1].source == Source(
sample=('test_plugin', 'samp_key')
)
def test_sample_hook(napari_plugin_manager):
viewer = ViewerModel()
napari_plugin_manager.discover_sample_data()
with pytest.raises(KeyError) as e:
viewer.open_sample('test_plugin', 'random data')
print([str(e)])
assert (
"Plugin 'test_plugin' does not provide sample data named 'random data'"
in str(e))
def _generate_random_data(shape=(512, 512)):
data = np.random.rand(*shape)
return [(data, {'name': 'random data'})]
LOGO = Path(napari.__file__).parent / 'resources' / 'logo.png'
class test_plugin:
@napari_hook_implementation
def napari_provide_sample_data():
return {
'random data': _generate_random_data,
'napari logo': LOGO,
'samp_key': {
'data': _generate_random_data,
'display_name': 'I look gorgeous in the menu!',
},
}
napari_plugin_manager.register(test_plugin)
reg = napari_plugin_manager._sample_data['test_plugin']
assert reg['random data']['data'] == _generate_random_data
assert reg['random data']['display_name'] == 'random data'
assert reg['napari logo']['data'] == LOGO
assert reg['napari logo']['display_name'] == 'napari logo'
assert reg['samp_key']['data'] == _generate_random_data
assert reg['samp_key']['display_name'] == 'I look gorgeous in the menu!'
assert len(viewer.layers) == 0
viewer.open_sample('test_plugin', 'random data')
assert viewer.layers[-1].source == Source(path=None,
reader_plugin=None,
sample=('test_plugin',
'random data'))
assert len(viewer.layers) == 1
viewer.open_sample('test_plugin', 'napari logo')
assert viewer.layers[-1].source == Source(
path=str(LOGO),
reader_plugin='builtins',
sample=('test_plugin', 'napari logo'),
)
assert len(viewer.layers) == 2
viewer.open_sample('test_plugin', 'samp_key')
assert viewer.layers[-1].source == Source(sample=('test_plugin',
'samp_key'))
assert len(viewer.layers) == 3
# test calling with kwargs
viewer.open_sample('test_plugin', 'samp_key', shape=(256, 256))
assert len(viewer.layers) == 4
assert viewer.layers[-1].source == Source(sample=('test_plugin',
'samp_key'))
def test_layer_source():
"""Test basic layer source assignment mechanism"""
with layer_source(path='some_path', reader_plugin='builtins'):
points = Points()
assert points.source == Source(path='some_path', reader_plugin='builtins')