def test_invalid_because_directory_not_readable():
if platform.system() == 'Windows' or not platform.system():
six.print_('Not running test as Windows doesnt do permissions.')
return
output_name = 'tests/output/'
if not os.path.exists(output_name):
os.mkdir(output_name)
dir_name = 'tests/output/unreadable'
if not os.path.exists(dir_name):
os.mkdir(dir_name)
print_dir_permissions(dir_name)
os.chmod(dir_name, 0o000)
print_dir_permissions(dir_name)
with pytest.raises(ValueError):
VTKSurfaceModelDirectoryLoader(dir_name)
os.chmod(dir_name, 0o100)
print_dir_permissions(dir_name)
with pytest.raises(ValueError):
VTKSurfaceModelDirectoryLoader(dir_name)
os.chmod(dir_name, 0o400)
print_dir_permissions(dir_name)
with pytest.raises(ValueError):
VTKSurfaceModelDirectoryLoader(dir_name)
os.chmod(dir_name, 0o500)
print_dir_permissions(dir_name)
VTKSurfaceModelDirectoryLoader(
dir_name) # should instantiate, but no data.
os.rmdir(dir_name)
def test_valid_dir_with_defaults_from_json():
dir_name = 'tests/data/models/Liver'
loader_no_json = VTKSurfaceModelDirectoryLoader(dir_name)
loader_with_json = VTKSurfaceModelDirectoryLoader(
dir_name, "tests/data/models/Liver/patient_defaults.json")
assert len(loader_no_json.models) == 9
assert len(loader_with_json.models) == 9
def add_vtk_models_from_dir(self, directory):
"""
Add VTK models to the foreground.
:param: directory, location of models
"""
model_loader = VTKSurfaceModelDirectoryLoader(directory)
self.vtk_overlay_window.add_vtk_models(model_loader.models)
def test_consistent_model_order_issue_89():
dir_name = 'tests/data/models/Liver'
loader = VTKSurfaceModelDirectoryLoader(dir_name)
# The name attribute should be a basename without extension
assert loader.models[0].get_name() == "arteries"
assert loader.models[3].get_name() == "gastric_vein"
assert loader.models[5].get_name() == "liver"
def populate_models(config):
"""
Loads vtk models from a directory and returns
a list of vtk actors and associated vtkPointLocators
:param: configuration, should contain a target value
:param: model_to_world: 4x4 matrix, of dtype float32
:return: locators
:return: actors
:raises: KeyError if target not in config
"""
models = []
if "target" not in config:
raise KeyError("Config must contain target key")
path_name = config.get("target")
loader = VTKSurfaceModelDirectoryLoader(path_name)
models = loader.models
locators = []
model_to_world = _set_model_to_world(config)
transform = vtk.vtkTransform()
transform.SetMatrix(np2vtk(model_to_world))
for model in models:
print(model.source.GetCenter())
transformer = vtk.vtkTransformPolyDataFilter()
transformer.SetTransform(transform)
transformer.SetInputData(model.source)
target = vtk.vtkPolyData()
transformer.SetOutput(target)
transformer.Update()
model.source = target
transformer.SetInputConnection(model.normals.GetOutputPort())
model.mapper = vtk.vtkPolyDataMapper()
model.mapper.SetInputConnection(transformer.GetOutputPort())
model.mapper.Update()
model.actor.SetMapper(model.mapper)
print("after trans", model.source.GetCenter())
point_locator = vtk.vtkPointLocator()
point_locator.SetDataSet(model.source)
point_locator.Update()
locators.append(point_locator)
return models, locators
def add_map(config):
"""
Loads vtk models from a directory and returns
a list of vtk actors, with mesh visualisation
:param: configuration, may contain a "map" key
:param: model_to_world: 4x4 matrix, of dtype float32
:return: actors, None if no "map" key
"""
models = []
if "map" not in config:
return None
path_name = config.get("map")
loader = VTKSurfaceModelDirectoryLoader(path_name)
models = loader.models
model_to_world = _set_model_to_world(config)
transform = vtk.vtkTransform()
transform.SetMatrix(np2vtk(model_to_world))
for model in models:
transformer = vtk.vtkTransformPolyDataFilter()
transformer.SetTransform(transform)
transformer.SetInputData(model.source)
target = vtk.vtkPolyData()
transformer.SetOutput(target)
transformer.Update()
model.source = target
transformer.SetInputConnection(model.normals.GetOutputPort())
model.mapper = vtk.vtkPolyDataMapper()
model.mapper.SetInputConnection(transformer.GetOutputPort())
model.mapper.Update()
model.actor.SetMapper(model.mapper)
model.actor.GetProperty().SetRepresentationToWireframe()
model.actor.GetProperty().SetColor(0.7, 0.7, 0.7)
model.actor.GetProperty().SetOpacity(1.0)
model.actor.GetProperty().SetBackfaceCulling(False)
return models
def test_valid_dir_with_colours_from_file_from_issue_4():
dir_name = 'tests/data/models/Liver'
loader = VTKSurfaceModelDirectoryLoader(dir_name)
assert len(loader.models) == 9
def test_valid_dir_with_default_colours():
dir_name = 'tests/data/models/Kidney'
loader = VTKSurfaceModelDirectoryLoader(dir_name)
assert len(loader.models) == 2
assert loader.models[0].get_colour() == loader.colours[str(0)]
assert loader.models[1].get_colour() == loader.colours[str(1)]
def test_invalid_because_empty_directory_name():
with pytest.raises(ValueError):
VTKSurfaceModelDirectoryLoader("")
def test_valid_dir_with_colours_model_file_doesnt_exist():
dir_name = 'tests/data/models/bad_colours'
with pytest.raises(FileNotFoundError):
loader = VTKSurfaceModelDirectoryLoader(dir_name)