def test_index(self):
# Arrange
active_layer = MockLayer(name="Layer 1", ndim=3)
layers = [
active_layer,
MockLayer(name="Layer 2", ndim=3),
MockLayer(name="Layer 3", ndim=3),
MockLayer(name="2D Layer", ndim=2),
]
channels = [Channel(0), Channel(1), Channel(2), Channel(3)]
workflows = [
create_autospec(WorkflowDefinition),
create_autospec(WorkflowDefinition),
create_autospec(WorkflowDefinition),
]
self._mock_viewer.get_layers.return_value = layers
self._mock_viewer.get_active_layer.return_value = [active_layer]
type(self._mock_workflow_engine).workflow_definitions = PropertyMock(
return_value=workflows)
self._mock_layer_reader.get_channels.return_value = channels
# Act
self._controller.index()
# Assert
self._mock_view_manager.load_view.assert_called_once_with(
self._controller.view, self._model)
assert self._controller.model.layers == [
"Layer 1", "Layer 2", "Layer 3"
]
assert self._controller.model.selected_layer == active_layer
assert self._controller.model.channels == channels
assert self._controller.model.workflows == workflows
def test_select_layer(self):
# Arrange
expected_layer = MockLayer(name="Layer 2")
layers = [
MockLayer(name="Layer 1", ndim=3), expected_layer,
MockLayer(name="Layer 3", ndim=3)
]
channels = [Channel(0), Channel(1), Channel(2), Channel(3)]
self._mock_viewer.get_layers.return_value = layers
self._mock_layer_reader.get_channels.return_value = channels
# Act
self._controller.select_layer("Layer 2")
# Assert
assert self._controller.model.selected_layer == expected_layer
def _get_channels_from_path(self, image_path: str) -> List[Channel]:
img = AICSImage(image_path)
img.set_scene(0)
channels = list()
for index, name in enumerate(img.channel_names):
channels.append(Channel(index, name))
return channels
def test_select_channel(self):
# Act
channel = Channel(0, "Brightfield")
self._controller.select_channel(channel)
# Assert
assert self._controller.model.selected_channel == channel
self._controller.view.update_workflows.assert_called_with(enabled=True)
def test_select_workflow(self):
# Arrange
layer0 = MockLayer("Layer 0", ndim=4)
expected_workflow = create_autospec(Workflow)
self._model.channels = [Channel(0), Channel(1), Channel(2), Channel(3)]
self._model.selected_channel = Channel(0)
self._model.selected_layer = MockLayer("Layer 1", ndim=4)
self._mock_workflow_engine.get_executable_workflow.return_value = expected_workflow
self._mock_viewer.add_image_layer.return_value = layer0
self._mock_layer_reader.get_channel_data.return_value = numpy.ones(
(75, 100, 100))
# Act
self._controller.select_workflow("sec61b")
# Assert
assert self._controller.model.active_workflow == expected_workflow
self._mock_router.workflow_steps.assert_called_once()
def test_close_workflow(self):
# Arrange
channel = Channel(0, "Brightfield")
self._controller.model.selected_channel = channel
# Act
self._controller.close_workflow()
# Assert
self._controller.model.selected_channel == None
self._mock_router.workflow_selection.assert_called_once()
def test_handle_layers_change_keeps_channels(self):
# Arrange
selected_layer = MockLayer(name="Layer 1", ndim=3)
layers = [
selected_layer,
MockLayer(name="Layer 2", ndim=3),
MockLayer(name="Layer 3", ndim=3),
]
selected_channel = Channel(3)
channels = [Channel(0), Channel(1), Channel(2), selected_channel]
self._mock_viewer.get_layers.return_value = layers
self._controller.model.channels = channels
self._controller.model.selected_layer = selected_layer
self._controller.model.selected_channel = selected_channel
# Act
self._controller._handle_layers_change(Event("test"))
# Assert
self._controller.model.layers == layers
self._controller.view.update_layers.assert_called_once()
self._controller.model.channels == channels
self._controller.model.selected_channel == selected_channel
def test_handle_layers_change_resets_channels(self):
# Arrange
layers = [
MockLayer(name="Layer 1", ndim=3),
MockLayer(name="Layer 2", ndim=3),
MockLayer(name="Layer 3", ndim=3),
]
self._mock_viewer.get_layers.return_value = layers
self._controller.model.channels = [
Channel(0), Channel(1),
Channel(2), Channel(3)
]
# Act
self._controller._handle_layers_change(Event("test"))
# Assert
self._controller.model.layers == layers
self._controller.view.update_layers.assert_called_once()
self._controller.model.channels is None
self._controller.model.selected_channel is None
self._controller.view.update_workflows.assert_called_with(
enabled=False)
def _get_channels_default(self, layer: Layer) -> List[Channel]:
if len(layer.data.shape) == 6:
# Has scenes
image_from_layer = [
layer.data[i, :, :, :, :, :]
for i in range(layer.data.shape[0])
]
else:
image_from_layer = layer.data
img = AICSImage(image_from_layer) # gives us a 6D image
img.set_scene(0)
index_c = img.dims.order.index("C")
channels = list()
for index in range(img.shape[index_c]):
channels.append(Channel(index))
return channels
def test_reset(self):
# Arrange
layers = ["layer 1", "layer 2"]
selected_layer = None
channels = ["channel 1", "channel 2"]
selected_channel = Channel(1, "channel 1")
workflows = ["laminb", "sec61b"]
active_workflow = "laminb"
model = SegmenterModel(layers, selected_layer, channels,
selected_channel, workflows, active_workflow)
# Act
model.reset()
# Assert
assert model.layers is None
assert model.selected_layer is None
assert model.channels is None
assert model.workflows is None
assert model.active_workflow is None