def test_inflation_and_deflation_of_area(surface_paths, percentage):
# Get default input
common_input = read_command_line_area(surface_paths[0], surface_paths[1])
# Change the default input
common_input.update(dict(method="area",
region_of_interest="first_line",
percentage=percentage,
smooth=False))
# Perform area manipulation
manipulate_area(**common_input)
# Import old area and splined centerline for region of interest
base_path = get_path_names(common_input['input_filepath'])
centerline_spline_path = base_path + "_centerline_spline.vtp"
centerline_area_spline_path = base_path + "_centerline_area_spline.vtp"
surface = read_polydata(common_input["output_filepath"])
centerline_area = read_polydata(centerline_area_spline_path)
centerline_spline = read_polydata(centerline_spline_path)
new_centerline_area, _ = vmtk_compute_centerline_sections(surface,
centerline_spline)
old_area = get_point_data_array("CenterlineSectionArea", centerline_area)
new_area = get_point_data_array("CenterlineSectionArea", new_centerline_area)
# Exclude first 5 %
old_area = old_area[int(0.1 * old_area.shape[0]):]
new_area = new_area[int(0.1 * new_area.shape[0]):]
# Change in radius
ratio = np.sqrt(new_area / old_area)
# Check if the altered area is equal has change according to percentage
assert np.mean(np.abs(ratio - (1 + percentage * 0.01))) < 0.05
def test_create_stenosis(surface_paths):
# Get default input
common_input = read_command_line_area(surface_paths[0], surface_paths[1])
# Get region points
base_path = get_path_names(common_input['input_filepath'])
centerline = extract_single_line(read_polydata(base_path + "_centerline.vtp"), 0)
n = centerline.GetNumberOfPoints()
region_point = list(centerline.GetPoint(int(n * 0.4)))
# Change default input
common_input.update(dict(region_of_interest="commandline",
region_points=region_point,
method="stenosis",
size=2.0,
percentage=50))
# Create a stenosis
manipulate_area(**common_input)
# Import old area and splined centerline for region of interest
base_path = get_path_names(common_input['input_filepath'])
centerline_spline_path = base_path + "_centerline_spline.vtp"
centerline_area_spline_path = base_path + "_centerline_area_spline.vtp"
new_surface_path = common_input["output_filepath"]
surface = read_polydata(new_surface_path)
centerline_area = read_polydata(centerline_area_spline_path)
centerline_spline = read_polydata(centerline_spline_path)
new_centerline_area, _ = vmtk_compute_centerline_sections(surface,
centerline_spline)
old_area = get_point_data_array("CenterlineSectionArea", centerline_area)
new_area = get_point_data_array("CenterlineSectionArea", new_centerline_area)
# Check if there is a 50 % narrowing
assert abs((np.sqrt(new_area / old_area)).min() - 0.5) < 0.05
def test_manipulate_branch_translation_and_polar_rotation(surface_paths):
# Get default input
common_input = read_command_line_branch(surface_paths[0], surface_paths[1])
# Arbitrary branch in model C0001
branch_number = 0
# No rotation around new surface normal vector
azimuth_angle0 = 0
# New location of branch
new_branch_location = (47.0, 27.8, 54.4)
# Branch translation method
translation_method = 'commandline'
# Change default input
common_input.update(
dict(branch_to_manipulate_number=branch_number, branch_location=new_branch_location,
translation_method=translation_method))
# Run without rotation around surface normal
common_input.update(dict(azimuth_angle=azimuth_angle0))
# Run area variation
manipulate_branch(**common_input)
# Set file paths
base_path = get_path_names(common_input['input_filepath'])
old_centerlines_path = base_path + "_centerline.vtp"
new_centerlines_path = base_path + "_centerline_moved.vtp"
# Read centerlines
old_centerlines = read_polydata(old_centerlines_path)
old_centerlines = [extract_single_line(old_centerlines, i) for i in range(old_centerlines.GetNumberOfLines())]
new_centerlines0 = read_polydata(new_centerlines_path)
new_centerlines0 = [extract_single_line(new_centerlines0, i) for i in range(new_centerlines0.GetNumberOfLines())]
# Perform same manipulation WITH rotation around new surface normal.
azimuth_angle1 = np.pi
common_input.update(dict(azimuth_angle=azimuth_angle1))
# Run manipulate branch
manipulate_branch(**common_input)
# Read centerlines
new_centerlines_path = base_path + "_centerline_moved_and_rotated.vtp"
new_centerlines1 = read_polydata(new_centerlines_path)
new_centerlines1 = [extract_single_line(new_centerlines1, i) for i in range(new_centerlines1.GetNumberOfLines())]
# Compare end point of all centerlines
unchanged_centerlines = compare_end_points(new_centerlines0, new_centerlines1)
unchanged_centerlines0 = compare_end_points(new_centerlines0, old_centerlines)
unchanged_centerlines1 = compare_end_points(new_centerlines1, old_centerlines)
assert len(unchanged_centerlines) < len(old_centerlines)
assert len(unchanged_centerlines0) < len(old_centerlines)
assert len(unchanged_centerlines1) < len(old_centerlines)
def test_manipulate_branch_translation(surface_paths):
# Get default input
common_input = read_command_line_branch(surface_paths[0], surface_paths[1])
# Opthalmic artery in model C0001
branch_number = 2
# No rotation around new surface normal vector
azimuth_angle = 0
# No rotation around new surface 'tangent' vector
polar_angle = 0
# New location of branch
new_branch_location = (45.7, 37.6, 42.5)
# Branch translation method
translation_method = 'commandline'
# Change default input
common_input.update(
dict(polar_angle=polar_angle, branch_to_manipulate_number=branch_number, branch_location=new_branch_location,
translation_method=translation_method, azimuth_angle=azimuth_angle))
# Run manipulate branch
manipulate_branch(**common_input)
# Set file paths
base_path = get_path_names(common_input['input_filepath'])
old_centerlines_path = base_path + "_centerline.vtp"
new_centerlines_path = base_path + "_centerline_moved.vtp"
# Read data, and get new area
old_centerlines = read_polydata(old_centerlines_path)
new_centerlines = read_polydata(new_centerlines_path)
old_centerlines = [extract_single_line(old_centerlines, i) for i in range(old_centerlines.GetNumberOfLines())]
new_centerlines = [extract_single_line(new_centerlines, i) for i in range(new_centerlines.GetNumberOfLines())]
untouched_centerlines = compare_end_points(old_centerlines, new_centerlines)
assert len(untouched_centerlines) < len(new_centerlines)
def test_manipulate_branch_azimuthal_rotation(surface_paths):
# Get default input
common_input = read_command_line_branch(surface_paths[0], surface_paths[1])
# Arbitrary branch in model C0001
branch_number = 2
# No rotation around new surface normal vector
azimuth_angle = np.pi
# Branch translation method
translation_method = 'no_translation'
# Change default input
common_input.update(
dict(branch_to_manipulate_number=branch_number, translation_method=translation_method))
# Run with only rotation around original surface normal
common_input.update(dict(azimuth_angle=azimuth_angle))
# Run manipulate branch
manipulate_branch(**common_input)
# Set file paths
base_path = get_path_names(common_input['input_filepath'])
old_centerlines_path = base_path + "_centerline.vtp"
new_centerlines_path = base_path + "_centerline_rotated.vtp"
# Read centerlines
old_centerlines = read_polydata(old_centerlines_path)
old_centerlines = [extract_single_line(old_centerlines, i) for i in range(old_centerlines.GetNumberOfLines())]
new_centerlines = read_polydata(new_centerlines_path)
new_centerlines = [extract_single_line(new_centerlines, i) for i in range(new_centerlines.GetNumberOfLines())]
# Compare end point of all centerlines
unchanged_centerlines = compare_end_points(new_centerlines, old_centerlines)
assert len(unchanged_centerlines) < len(old_centerlines)
def test_area_linear(surface_paths):
# Get default input
common_input = read_command_line_area(surface_paths[0], surface_paths[1])
# Set region points
base_path = get_path_names(common_input['input_filepath'])
centerline = extract_single_line(read_polydata(base_path + "_centerline.vtp"), 0)
n = centerline.GetNumberOfPoints()
region_points = list(centerline.GetPoint(int(n * 0.3))) + list(centerline.GetPoint(int(n * 0.4)))
# Change default input
common_input.update(dict(region_of_interest="commandline",
region_points=region_points,
method="linear",
smooth=False,
size=1,
percentage=50))
# Run area variation
manipulate_area(**common_input)
# Set file paths
base_path = get_path_names(common_input['input_filepath'])
centerline_spline_path = base_path + "_centerline_spline.vtp"
new_surface_path = common_input["output_filepath"]
# Read data, and get new area
surface = read_polydata(new_surface_path)
centerline_spline = read_polydata(centerline_spline_path)
new_centerline_area, _ = vmtk_compute_centerline_sections(surface,
centerline_spline)
length = get_curvilinear_coordinate(centerline_spline)
new_area = get_point_data_array("CenterlineSectionArea", new_centerline_area)
linear_change = new_area[0] + (new_area[-1] - new_area[0]) * (length / length.max())
# Check if the new area is within 2 % of the expected value
assert (np.abs(new_area[:, 0] - linear_change) / linear_change).max() < 0.02
def test_area_variation(ratio, surface_paths):
# Get default input
common_input = read_command_line_area(surface_paths[0], surface_paths[1])
# Set region points
base_path = get_path_names(common_input['input_filepath'])
centerline = extract_single_line(read_polydata(base_path + "_centerline.vtp"), 0)
n = centerline.GetNumberOfPoints()
region_points = list(centerline.GetPoint(int(n * 0.05))) + list(centerline.GetPoint(int(n * 0.5)))
# Change default input
common_input.update(dict(method="variation",
smooth=False,
region_of_interest="commandline",
region_points=region_points,
ratio=ratio,
beta=None))
# Run area variation
manipulate_area(**common_input)
# Set file paths
base_path = get_path_names(common_input['input_filepath'])
centerline_spline_path = base_path + "_centerline_spline.vtp"
new_surface_path = common_input["output_filepath"]
# Read data, and get new area
surface = read_polydata(new_surface_path)
centerline_spline = read_polydata(centerline_spline_path)
new_centerline_area, _ = vmtk_compute_centerline_sections(surface,
centerline_spline)
new_area = get_point_data_array("CenterlineSectionArea", new_centerline_area)
# Check if the new ratio holds
assert abs(ratio - new_area.max() / new_area.min()) < 0.15