diffusion_utils.py File Reference

Namespaces
namespace	diffusion_utils

Functions
	diffusion_utils.row_reduce_matrix (A, GF)
	diffusion_utils.solve_linear_system_with_boundary (B, v, A, A_red, V, GF)
	diffusion_utils.solve_linear_system (B, v)
	diffusion_utils.cut_path_from_bottom (path, h, grid, axis=-1)
	diffusion_utils.cut_path_from_top (path, h, grid, axis=-1)
	diffusion_utils.get_cmap (n, name='hsv')
	diffusion_utils.get_box_from_cell (cell_file)
	diffusion_utils.out_to_atoms (inputfile, backbone_atoms, flow_atoms)
	DEPRECATED?
	diffusion_utils.clean_Li (Li, m, M)
	diffusion_utils.make_geodesics (grid, r, M, m, axes, dim, D_=None, D_force_graph_=None, verbose=False)
	diffusion_utils.find_geod (idx0, idx1, geodesics, pts, D, maxiter=np.inf)
	diffusion_utils.dist_periodic_boundaries (grid_, M, m, axes, dim=3)
	diffusion_utils.dist_from_pts_periodic_boundaries (pts_, grid_, M, m, axes, dim=3)
	diffusion_utils.append_tr (ITRIS, B, edge_idxs, ia, ib, ic)
	diffusion_utils.check_tr (p0, p1, p2, res_grid, grid, cubic_to_res, ITRIS, B, edge_idxs)
	diffusion_utils.r_squared (px, py, pz, balls_centres, balls_radii)
	diffusion_utils.aux_fn (px, py, pz, xc, yc, zc, r, eps, p=4)
	diffusion_utils.grad_r2 (pt, balls_centres, balls_radii, p=2, eps=1)
	diffusion_utils.sample_path (idx, N, res_grid, z_1, maxiter=100000)
	diffusion_utils.smooth_path (path, geod, res_grid, D)
	diffusion_utils.close_paths (p_0, p_1, grid, geod, D)
	diffusion_utils.homological_simplification_of_path_pts (idx0, idx1, path, grid, geod, V, rank, GF, D, N, edge_idxs, r_graph)
	diffusion_utils.homological_simplification_of_path (path, grid, geod, V, rank, GF, D, N, edge_idxs, r_graph)
	diffusion_utils.close_paths_A_0_A_1 (p_0, p_1, D, A_0, A_1, res_to_A_0, res_to_A_1, A_0_to_res, A_1_to_res, geod_A_0, geod_A_1)
	diffusion_utils.join_points_boundary_conditions (p_, q_, M, m, axes, dim, n=20)
	diffusion_utils.close_paths_boundary_conditions (p_0, p_1, res_grid, geod, M, m, D, axes, dim)
	diffusion_utils.close_deadlocks (p_0, p_1, res_grid, geod, res_to_A_0, A_0_to_res, geod_A_0, A_0)
	diffusion_utils.simplify_path (path_)
	diffusion_utils.path_to_vec (path, D, N_1, edge_idxs, r_graph, verbose=False)
	diffusion_utils.equivalence (A, v_path, rank)
	diffusion_utils.project_path (path_coords, grid)
	diffusion_utils.project_path_periodic (path_coords, grid, M, m, axes, dim=3, D_=None)
	diffusion_utils.project_timeseries_array (A, grid, M, m, axes, dim=3)
	diffusion_utils.cluster_deadlocks (PATHS, res_grid, geod, res_to_A_0, geod_A_0, A_0)
	diffusion_utils.save_paths (LIST, name, folder_path)
	diffusion_utils.compute_all (LIST)
	diffusion_utils.compute_penalties (LIST)
	diffusion_utils.compute_direction (LIST)
	diffusion_utils.compute_repulsion (LIST)
	diffusion_utils.find_geod_wrap (LIST)
	diffusion_utils.rank_mod_p (LIST)