def test_regression_test1():
"""A regression test with manually init"""
parameters = [136.0, 151.0, -91.0, 8.0]
model = VTKSurfaceModel("data/CT_Level_1.vtp", [1., 0., 0.])
x_values = model.get_points_as_numpy()[:, 0]
y_values = model.get_points_as_numpy()[:, 1]
z_values = model.get_points_as_numpy()[:, 2]
result = sphere_fitting.fit_sphere_least_squares(x_values, y_values,
z_values, parameters)
numpy.testing.assert_approx_equal(result.x[0], 136.571, significant=3)
numpy.testing.assert_approx_equal(result.x[1], 151.973, significant=3)
numpy.testing.assert_approx_equal(result.x[2], -95.518, significant=3)
numpy.testing.assert_approx_equal(result.x[3], 8.119, significant=3)
def run_demo(model_file_name, output="", configfile=False):
""" Run the application """
model = VTKSurfaceModel(model_file_name, [1., 0., 0.])
x_values = model.get_points_as_numpy()[:, 0]
y_values = model.get_points_as_numpy()[:, 1]
z_values = model.get_points_as_numpy()[:, 2]
initial_parameters = [
mean(x_values),
mean(y_values),
mean(z_values),
std(x_values)
]
bounds = ((-inf, -inf, -inf, -inf), (inf, inf, inf, inf))
if configfile:
configurer = ConfigurationManager(configfile)
configuration = configurer.get_copy()
if "initial values" in configuration:
initial_parameters = configuration.get("initial values")
if "bounds" in configuration:
bounds = configuration.get("bounds")
if "fixed radius" in configuration:
radius = configuration.get("fixed radius")
bounds = ((-inf, -inf, -inf, radius - 1e-6), (inf, inf, inf,
radius + 1e-6))
result = sphere_fitting.fit_sphere_least_squares(x_values,
y_values,
z_values,
initial_parameters,
bounds=bounds)
print("Result is {}".format(result))
if output != "":
sphere = vtk.vtkSphereSource()
sphere.SetCenter(result.x[0], result.x[1], result.x[2])
sphere.SetRadius(result.x[3])
sphere.SetThetaResolution(60)
sphere.SetPhiResolution(60)
writer = vtk.vtkXMLPolyDataWriter()
writer.SetFileName(output)
writer.SetInputData(sphere.GetOutput())
sphere.Update()
writer.Write()
def test_extract_points_and_normals_as_numpy_array():
input_file = 'tests/data/models/Prostate.vtk'
model = VTKSurfaceModel(input_file, colors.red)
number_of_points = model.get_number_of_points()
points = model.get_points_as_numpy()
assert isinstance(points, np.ndarray)
assert points.shape[0] == number_of_points
assert points.shape[1] == 3
normals = model.get_normals_as_numpy()
assert isinstance(normals, np.ndarray)
assert normals.shape[0] == number_of_points
assert normals.shape[1] == 3
def test_regression_test2():
"""A regression test with fixed radius"""
model = VTKSurfaceModel("data/US_Sphere_2.vtp", [1., 0., 0.])
x_values = model.get_points_as_numpy()[:, 0]
y_values = model.get_points_as_numpy()[:, 1]
z_values = model.get_points_as_numpy()[:, 2]
parameters = [
numpy.mean(x_values),
numpy.mean(y_values),
numpy.mean(z_values), 4.5
]
radius = 4.5
epsilon = 1e-6
bounds = ((-numpy.inf, -numpy.inf, -numpy.inf, radius - epsilon),
(numpy.inf, numpy.inf, numpy.inf, radius + epsilon))
result = sphere_fitting.fit_sphere_least_squares(x_values,
y_values,
z_values,
parameters,
bounds=bounds)
numpy.testing.assert_approx_equal(result.x[0], 86.474, significant=3)
numpy.testing.assert_approx_equal(result.x[1], -97.243, significant=3)
numpy.testing.assert_approx_equal(result.x[2], -208.528, significant=3)
numpy.testing.assert_approx_equal(result.x[3], 4.500, significant=3)