svcco.branch_addition package

Submodules

svcco.branch_addition.add_bifurcation module

svcco.branch_addition.add_bifurcation.add_bifurcation(tree, parent_edge, candidate_point, results, optimum, isforest=False)[source]
svcco.branch_addition.add_bifurcation.update_index(sub_division_index, main_idx)[source]

svcco.branch_addition.add_branches module

svcco.branch_addition.add_branches.add_branch(data, boundary_within=None, edge_number=None, gamma=None, nu=None, Qterm=None, Pperm=None, Pterm=None, lam=None, k=None, mu=None, boundary_threshold=None, threshold_adjuster=0.75, threshold_exponent=1.5, max_skip=None, target_low=None, target_high=None, sub_division_map=None, sub_division_index=None, level_func=None, func=None, func_grad=None, active_patches=None, patch_tree=None, patch_centers=None, fraction=None, isforest=False)[source]

svcco.branch_addition.add_branches_v2 module

svcco.branch_addition.add_branches_v2.add_branch(data, boundary, edge_number=None, gamma=None, nu=None, Qterm=None, Pperm=None, Pterm=None, lam=None, k=None, mu=None, threshold_adjuster=0.9, threshold_exponent=0.5, max_skip=None, target_low=None, target_high=None, sub_division_map=None, sub_division_index=None, fraction=None, isforest=False, ishomogeneous=None, isconvex=None, isdirected=None, isclamped=None, radius_buffer=None)[source]

svcco.branch_addition.add_branches_v3 module

svcco.branch_addition.add_branches_v3.add_branch(tree, low, high, threshold_exponent=1.5, threshold_adjuster=0.75, all_max_attempts=40, max_attemps=10, sampling=20, max_skip=8, flow_ratio=None, radius_buffer=0, isforest=False, threshold=None, radius_scale=4, method='L-BFGS-B')[source]

svcco.branch_addition.add_depths module

svcco.branch_addition.add_depths.add_depths(data, edge)[source]

svcco.branch_addition.add_edge module

svcco.branch_addition.add_edge.add_edge(data, proximal, distal, parent, flow, proximal_idx=-1.0, distal_idx=-1.0, left_child=-1.0, right_child=-1.0)[source]

svcco.branch_addition.add_flow module

svcco.branch_addition.add_flow.add_flow(data, parent, flow)[source]

svcco.branch_addition.add_geodesic_path module

svcco.branch_addition.add_geodesic_path.add_geodesic_path(data, path, lengths, parent_vessel_idx, Qterm, gamma, nu, Pperm, Pterm, sub_division_index, sub_division_map)[source]

svcco.branch_addition.basis module

svcco.branch_addition.basis.basis(data, edges)[source]
svcco.branch_addition.basis.tangent_basis(normal, pt)[source]

svcco.branch_addition.calculate_length module

svcco.branch_addition.calculate_length.length(data, edge)[source]

svcco.branch_addition.calculate_radii module

svcco.branch_addition.calculate_radii.radii(data, Pperm, Pterm)[source]
svcco.branch_addition.calculate_radii.update_radii(data, Pperm, Pterm)[source]

svcco.branch_addition.check module

svcco.branch_addition.check.check(data, point_set, threshold)[source]
svcco.branch_addition.check.check_point(data, point, threshold)[source]

svcco.branch_addition.close module

svcco.branch_addition.close.close(data, point, N=20)[source]
svcco.branch_addition.close.close_binary_vectorize(data, point)[source]
svcco.branch_addition.close.close_binary_vectorize2(data, point)[source]
svcco.branch_addition.close.close_exact(data, point)[source]

svcco.branch_addition.finite_difference module

svcco.branch_addition.finite_difference.finite_difference(data, precomputed, terminal, vessel, gamma, nu, Qterm, Pperm, Pterm)[source]
svcco.branch_addition.finite_difference.finite_difference_naive(data, precomputed, terminal, vessel, gamma, nu, Qterm, Pperm, Pterm)[source]

svcco.branch_addition.geodesic module

svcco.branch_addition.geodesic.extract_surface(msh)[source]
svcco.branch_addition.geodesic.geodesic(polydata, proximal, distal, terminal, bifurcation)[source]

svcco.branch_addition.get_path module

svcco.branch_addition.get_path.get_path(D, Pr, i, j)[source]

svcco.branch_addition.get_point module

svcco.branch_addition.get_point.sample_area(segment_data, term, grad, fraction)[source]
svcco.branch_addition.get_point.to_point(start, end, grad, fraction, hess=None)[source]

svcco.branch_addition.local_func_v5 module

svcco.branch_addition.local_func_v5.fast_local_function(data, terminal_point, edge, gamma, nu, Qterm, Pperm, Pterm, precomputed=None)[source]
svcco.branch_addition.local_func_v5.fast_point(a, b, n=array([1.0, 1.0, 1.0]), e1=array([0.0, 0.0, 0.0]), p_0=array([0.0, 0.0, 0.0]))[source]

svcco.branch_addition.local_func_v6 module

svcco.branch_addition.local_func_v6.fast_local_function(data, mesh, terminal, edge, gamma, nu, Qterm, Pperm, Pterm)[source]

svcco.branch_addition.local_func_v7 module

svcco.branch_addition.local_func_v7.constructor(data, terminal, edge, gamma, nu, Qterm, Pperm, Pterm, lam, mu, maxiter, method='L-BFGS-B')[source]
svcco.branch_addition.local_func_v7.fast_local_function(data, mesh, terminal, edge, gamma, nu, Qterm, Pperm, Pterm)[source]
svcco.branch_addition.local_func_v7.fast_local_function_test(data, mesh, terminal, edge, gamma, nu, Qterm, Pperm, Pterm)[source]
svcco.branch_addition.local_func_v7.path(data, edge)[source]
svcco.branch_addition.local_func_v7.volume(x, data, terminal, edge, gamma, nu, Qterm, Pperm, Pterm)[source]

svcco.branch_addition.sample_triad module

svcco.branch_addition.sample_triad.sample_triad(p1, p2, p3)[source]
svcco.branch_addition.sample_triad.triangle_subdivide(triangles, i=1)[source]
svcco.branch_addition.sample_triad.unique_triangle_points(triangles)[source]

svcco.branch_addition.set_root module

svcco.branch_addition.set_root.set_root(data, boundary, Qterm, gamma, nu, Pperm, Pterm, fraction, ishomogeneous, isconvex, isdirected, start, direction, limit_high, limit_low, volume, low=-1, high=0, niter=200)[source]

Explaination of code

svcco.branch_addition.set_root_homogeneous_nonconvex module

svcco.branch_addition.set_root_homogeneous_nonconvex.set_root_homogeneous_nonconvex(data, boundary, Qterm, gamma, nu, Pperm, Pterm, start, direction)[source]

svcco.branch_addition.triangle module

svcco.branch_addition.triangle.absolute_length_constraint()[source]
svcco.branch_addition.triangle.angle_constraint(p0, p1, p2, constraint, greater)[source]
svcco.branch_addition.triangle.boundary_constraint(p0, boundary, patches)[source]
svcco.branch_addition.triangle.get_local_points(data, vessel, terminal, num, isclamped)[source]
svcco.branch_addition.triangle.relative_length_constraint(p0, p1, p2, p3, ratio)[source]

svcco.branch_addition.update module

svcco.branch_addition.update.naive(data, gamma, nu, start)[source]
svcco.branch_addition.update.update(data, gamma, nu)[source]

svcco.branch_addition.update_geodesic module

svcco.branch_addition.update_geodesic.update_geodesic(data, gamma, nu)[source]

Module contents