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| import numpy as np | |
| # from scipy import weave | |
| def calc_scatters(K): | |
| n = K.shape[0] | |
| K1 = np.cumsum([0] + list(np.diag(K))) | |
| K2 = np.zeros((n+1, n+1)) | |
| K2[1:, 1:] = np.cumsum(np.cumsum(K, 0), 1) # TODO: use the fact that K - symmetric | |
| scatters = np.zeros((n, n)) | |
| # code = r""" | |
| # for (int i = 0; i < n; i++) { | |
| # for (int j = i; j < n; j++) { | |
| # scatters(i,j) = K1(j+1)-K1(i) - (K2(j+1,j+1)+K2(i,i)-K2(j+1,i)-K2(i,j+1))/(j-i+1); | |
| # } | |
| # } | |
| # """ | |
| # weave.inline(code, ['K1','K2','scatters','n'], global_dict = \ | |
| # {'K1':K1, 'K2':K2, 'scatters':scatters, 'n':n}, type_converters=weave.converters.blitz) | |
| for i in range(n): | |
| for j in range(i, n): | |
| scatters[i,j] = K1[j+1] - K1[i] - (K2[j+1,j+1]+K2[i,i]-K2[j+1,i]-K2[i,j+1])/(j-i+1) | |
| return scatters | |
| def cpd_nonlin(K, ncp, lmin=1, lmax=100000, backtrack=True, verbose=True, | |
| out_scatters=None): | |
| """ Change point detection with dynamic programming | |
| K - square kernel matrix | |
| ncp - number of change points to detect (ncp >= 0) | |
| lmin - minimal length of a segment | |
| lmax - maximal length of a segment | |
| backtrack - when False - only evaluate objective scores (to save memory) | |
| Returns: (cps, obj) | |
| cps - detected array of change points: mean is thought to be constant on [ cps[i], cps[i+1] ) | |
| obj_vals - values of the objective function for 0..m changepoints | |
| """ | |
| m = int(ncp) # prevent numpy.int64 | |
| (n, n1) = K.shape | |
| assert(n == n1), "Kernel matrix awaited." | |
| assert(n >= (m + 1)*lmin) | |
| assert(n <= (m + 1)*lmax) | |
| assert(lmax >= lmin >= 1) | |
| if verbose: | |
| #print "n =", n | |
| print("Precomputing scatters...") | |
| J = calc_scatters(K) | |
| if out_scatters != None: | |
| out_scatters[0] = J | |
| if verbose: | |
| print("Inferring best change points...") | |
| I = 1e101*np.ones((m+1, n+1)) | |
| I[0, lmin:lmax] = J[0, lmin-1:lmax-1] | |
| if backtrack: | |
| p = np.zeros((m+1, n+1), dtype=int) | |
| else: | |
| p = np.zeros((1,1), dtype=int) | |
| # code = r""" | |
| # #define max(x,y) ((x)>(y)?(x):(y)) | |
| # for (int k=1; k<m+1; k++) { | |
| # for (int l=(k+1)*lmin; l<n+1; l++) { | |
| # I(k, l) = 1e100; //nearly infinity | |
| # for (int t=max(k*lmin,l-lmax); t<l-lmin+1; t++) { | |
| # double c = I(k-1, t) + J(t, l-1); | |
| # if (c < I(k, l)) { | |
| # I(k, l) = c; | |
| # if (backtrack == 1) { | |
| # p(k, l) = t; | |
| # } | |
| # } | |
| # } | |
| # } | |
| # } | |
| # """ | |
| # weave.inline(code, ['m','n','p','I', 'J', 'lmin', 'lmax', 'backtrack'], \ | |
| # global_dict={'m':m, 'n':n, 'p':p, 'I':I, 'J':J, \ | |
| # 'lmin':lmin, 'lmax':lmax, 'backtrack': int(1) if backtrack else int(0)}, | |
| # type_converters=weave.converters.blitz) | |
| for k in range(1, m+1): | |
| for l in range((k+1)*lmin, n+1): | |
| I[k, l] = 1e100 | |
| for t in range(max(k*lmin,l-lmax), l-lmin+1): | |
| c = I[k-1, t] + J[t, l-1] | |
| if (c < I[k, l]): | |
| I[k, l] = c | |
| if (backtrack == 1): | |
| p[k, l] = t | |
| # Collect change points | |
| cps = np.zeros(m, dtype=int) | |
| if backtrack: | |
| cur = n | |
| for k in range(m, 0, -1): | |
| cps[k-1] = p[k, cur] | |
| cur = cps[k-1] | |
| scores = I[:, n].copy() | |
| scores[scores > 1e99] = np.inf | |
| return cps, scores | |