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_automated_landmarking(surface_paths, algorithm):
# Get region points
base_path = get_path_names(surface_paths[0])
relevant_outlets = [35.8, 59.8, 39.7, 76.8, 54.7, 53.2]
ica_centerline = extract_ica_centerline(base_path,
surface_paths[0],
0.1,
relevant_outlets=relevant_outlets)
landmark_input = dict(centerline=ica_centerline,
base_path=base_path,
approximation_method="spline",
algorithm=algorithm,
resampling_step=0.1,
smooth_line=False,
nknots=8,
iterations=100)
if algorithm == "bogunovic":
landmark_input.update(smoothing_factor=1.0, coronal_axis='z')
landmarks = landmarking_bogunovic(**landmark_input)
assert len(landmarks) == 4
if algorithm == "piccinelli":
landmark_input.update(smoothing_factor_torsion=1.0,
smoothing_factor_curv=1.0)
landmarks = landmarking_piccinelli(**landmark_input)
assert len(landmarks) > 0
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_siphon(surface_paths, alpha, beta):
# Set problem specific parameters
common_input = read_command_line_bend(surface_paths[0], surface_paths[1])
common_input.update(
dict(alpha=alpha,
beta=beta,
region_of_interest="commandline",
region_points=[
44.17085266113281, 38.514854431152344, 41.20818328857422,
43.242130279541016, 42.68572235107422, 38.65191650390625
]))
# Perform manipulation
manipulate_bend(**common_input)
# Compute angle
base_path = get_path_names(common_input['input_filepath'])
new_centerlines_path = base_path + "_centerlines_alpha_%s_beta_%s.vtp" % (
alpha, beta)
new_centerlines = read_polydata(new_centerlines_path)
angle_new, angle_original = compute_angle(
common_input["input_filepath"],
alpha,
beta,
"plane",
new_centerlines,
region_of_interest=common_input["region_of_interest"],
region_points=common_input["region_points"])
if alpha < 0 and beta == 0 or beta > 0 and alpha == 0:
assert angle_original < angle_new
elif alpha > 0 and beta == 0 or beta < 0 and alpha == 0:
assert angle_original > angle_new
else:
assert angle_original > angle_new
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_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_decrease_curvature(surface_paths, smooth_line):
# Get default inputs
common_input = read_command_line_curvature(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"), 1)
n = centerline.GetNumberOfPoints()
region_points = list(centerline.GetPoint(int(n * 0.1))) + list(centerline.GetPoint(int(n * 0.4)))
# Set problem specific parameters
common_input.update(dict(smooth_factor_line=1.5,
iterations=200,
region_of_interest="commandline",
region_points=region_points,
smooth_line=smooth_line))
# Manipulate surface
manipulate_curvature(**common_input)
# Select and compare altered region
p1 = np.asarray(region_points[:3])
p2 = np.asarray(region_points[3:])
old_centerlines_path = base_path + "_centerline.vtp"
old_centerlines = read_polydata(old_centerlines_path)
old_locator = get_vtk_point_locator(extract_single_line(old_centerlines, 0))
old_id1 = old_locator.FindClosestPoint(p1)
old_id2 = old_locator.FindClosestPoint(p2)
old_centerline = extract_single_line(old_centerlines, 0, start_id=old_id1,
end_id=old_id2)
direction = "smoothed" if smooth_line else "extended"
new_centerlines_path = base_path + "_centerline_new_%s.vtp" % direction
new_centerlines = read_polydata(new_centerlines_path)
new_locator = get_vtk_point_locator(extract_single_line(new_centerlines, 0))
new_id1 = new_locator.FindClosestPoint(p1)
new_id2 = new_locator.FindClosestPoint(p2)
new_centerline = extract_single_line(new_centerlines, 0, start_id=new_id1,
end_id=new_id2)
# Comute curvature and assert
_, old_curvature = compute_discrete_derivatives(old_centerline, neigh=20)
_, new_curvature = compute_discrete_derivatives(new_centerline, neigh=20)
old_mean_curv = np.mean(old_curvature)
new_mean_curv = np.mean(new_curvature)
if smooth_line:
assert old_mean_curv > new_mean_curv
else:
assert old_mean_curv < new_mean_curv
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
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_bifurcation_angle(surface_paths, angle):
common_input = read_command_line_bifurcation(surface_paths[0],
surface_paths[1])
common_input.update(
dict(angle=angle,
region_of_interest="commandline",
region_points=[35.8, 59.8, 39.7, 76.8, 54.7, 53.2]))
manipulate_bifurcation(**common_input)
# Read in files to compute angle
base_path = get_path_names(common_input["input_filepath"])
old_centerlines = read_polydata(base_path + "_centerline_par.vtp")
new_centerlines = read_polydata(base_path +
"_centerline_interpolated_ang.vtp")
end_points = read_polydata(base_path + "_clippingpoints.vtp")
# Start points
start_point1 = end_points.GetPoint(1)
start_point2 = end_points.GetPoint(2)
# Get relevant centerlines
cl_old_1 = -1
cl_old_2 = -1
cl_new_1 = -1
cl_new_2 = -1
tol = get_centerline_tolerance(old_centerlines)
for i in range(old_centerlines.GetNumberOfLines()):
line_old = extract_single_line(old_centerlines, i)
line_new = extract_single_line(new_centerlines, i)
loc_old = get_vtk_point_locator(line_old)
loc_new = get_vtk_point_locator(line_new)
id1_old = loc_old.FindClosestPoint(start_point1)
id2_old = loc_old.FindClosestPoint(start_point2)
id1_new = loc_new.FindClosestPoint(start_point1)
id2_new = loc_new.FindClosestPoint(start_point2)
if get_distance(start_point1, line_old.GetPoint(id1_old)) < tol:
cl_old_1 = i
cl_old_id1 = id1_old
if get_distance(start_point2, line_old.GetPoint(id2_old)) < tol:
cl_old_2 = i
cl_old_id2 = id2_old
if get_distance(start_point1, line_new.GetPoint(id1_new)) < tol:
cl_new_1 = i
cl_new_id1 = id1_new
if get_distance(start_point2, line_new.GetPoint(id2_new)) < tol:
cl_new_2 = i
cl_new_id2 = id2_new
if -1 not in [cl_old_1, cl_old_2, cl_new_1, cl_new_2]:
break
# Get end points
end_point1_old = np.array(
extract_single_line(old_centerlines,
cl_old_1).GetPoint(cl_old_id1 + 20))
end_point2_old = np.array(
extract_single_line(old_centerlines,
cl_old_2).GetPoint(cl_old_id2 + 20))
end_point1_new = np.array(
extract_single_line(new_centerlines,
cl_new_1).GetPoint(cl_new_id1 + 20))
end_point2_new = np.array(
extract_single_line(new_centerlines,
cl_new_2).GetPoint(cl_new_id2 + 20))
# Vectors
v1_old = end_point1_old - np.array(start_point1)
v2_old = end_point2_old - np.array(start_point2)
v1_new = end_point1_new - np.array(start_point1)
v2_new = end_point2_new - np.array(start_point2)
# Normalize
v1_old = v1_old / np.sqrt(np.sum(v1_old**2))
v2_old = v2_old / np.sqrt(np.sum(v2_old**2))
v1_new = v1_new / np.sqrt(np.sum(v1_new**2))
v2_new = v2_new / np.sqrt(np.sum(v2_new**2))
# Angle
first_daughter_branch_angle_change = np.arccos(np.dot(v1_old, v1_new))
second_daughter_branch_angle_change = np.arccos(np.dot(v2_old, v2_new))
assert abs(first_daughter_branch_angle_change +
second_daughter_branch_angle_change -
2 * abs(common_input["angle"])) < 0.04