# Helpers for current-flow betweenness and current-flow closness # Lazy computations for inverse Laplacian and flow-matrix rows. import networkx as nx def flow_matrix_row(G, weight=None, dtype=float, solver="lu"): # Generate a row of the current-flow matrix import numpy as np solvername = { "full": FullInverseLaplacian, "lu": SuperLUInverseLaplacian, "cg": CGInverseLaplacian, } n = G.number_of_nodes() L = nx.laplacian_matrix(G, nodelist=range(n), weight=weight).asformat("csc") L = L.astype(dtype) C = solvername[solver](L, dtype=dtype) # initialize solver w = C.w # w is the Laplacian matrix width # row-by-row flow matrix for u, v in sorted(sorted((u, v)) for u, v in G.edges()): B = np.zeros(w, dtype=dtype) c = G[u][v].get(weight, 1.0) B[u % w] = c B[v % w] = -c # get only the rows needed in the inverse laplacian # and multiply to get the flow matrix row row = B @ C.get_rows(u, v) yield row, (u, v) # Class to compute the inverse laplacian only for specified rows # Allows computation of the current-flow matrix without storing entire # inverse laplacian matrix class InverseLaplacian: def __init__(self, L, width=None, dtype=None): global np import numpy as np (n, n) = L.shape self.dtype = dtype self.n = n if width is None: self.w = self.width(L) else: self.w = width self.C = np.zeros((self.w, n), dtype=dtype) self.L1 = L[1:, 1:] self.init_solver(L) def init_solver(self, L): pass def solve(self, r): raise nx.NetworkXError("Implement solver") def solve_inverse(self, r): raise nx.NetworkXError("Implement solver") def get_rows(self, r1, r2): for r in range(r1, r2 + 1): self.C[r % self.w, 1:] = self.solve_inverse(r) return self.C def get_row(self, r): self.C[r % self.w, 1:] = self.solve_inverse(r) return self.C[r % self.w] def width(self, L): m = 0 for i, row in enumerate(L): w = 0 x, y = np.nonzero(row) if len(y) > 0: v = y - i w = v.max() - v.min() + 1 m = max(w, m) return m class FullInverseLaplacian(InverseLaplacian): def init_solver(self, L): self.IL = np.zeros(L.shape, dtype=self.dtype) self.IL[1:, 1:] = np.linalg.inv(self.L1.todense()) def solve(self, rhs): s = np.zeros(rhs.shape, dtype=self.dtype) s = self.IL @ rhs return s def solve_inverse(self, r): return self.IL[r, 1:] class SuperLUInverseLaplacian(InverseLaplacian): def init_solver(self, L): import scipy as sp import scipy.sparse.linalg # call as sp.sparse.linalg self.lusolve = sp.sparse.linalg.factorized(self.L1.tocsc()) def solve_inverse(self, r): rhs = np.zeros(self.n, dtype=self.dtype) rhs[r] = 1 return self.lusolve(rhs[1:]) def solve(self, rhs): s = np.zeros(rhs.shape, dtype=self.dtype) s[1:] = self.lusolve(rhs[1:]) return s class CGInverseLaplacian(InverseLaplacian): def init_solver(self, L): global sp import scipy as sp import scipy.sparse.linalg # call as sp.sparse.linalg ilu = sp.sparse.linalg.spilu(self.L1.tocsc()) n = self.n - 1 self.M = sp.sparse.linalg.LinearOperator(shape=(n, n), matvec=ilu.solve) def solve(self, rhs): s = np.zeros(rhs.shape, dtype=self.dtype) s[1:] = sp.sparse.linalg.cg(self.L1, rhs[1:], M=self.M, atol=0)[0] return s def solve_inverse(self, r): rhs = np.zeros(self.n, self.dtype) rhs[r] = 1 return sp.sparse.linalg.cg(self.L1, rhs[1:], M=self.M, atol=0)[0]