dim mclgTFexecx ( mclx* mx , mclgTF* tf , mcxbool allow_graph_ops ) { dim offset = 0, k = 0 ; mclpAR* par_edge = tf->par_edge ; mclpAR* par_graph = tf->par_graph ; while (offset < par_edge->n_ivps || k < par_graph->n_ivps) { dim top = offset ; while (top < par_edge->n_ivps && par_edge->ivps[top].idx != MCLX_UNARY_UNUSED) top++ ; if (top > offset) { mclpAR* par = mclpARfromIvps(NULL, par_edge->ivps+offset, top-offset) ;fprintf(stderr, "unary exec %d %d\n", (int) offset, (int) top) ; mclxUnaryList(mx, par) ; mclpARfree(&par) ; } if (par_edge->ivps[top].idx == MCLX_UNARY_UNUSED) { if (k >= par_graph->n_ivps) { mcxErr("mclgTFexec", "off the rails") ; break ; } if (allow_graph_ops) mclgTFgraph(mx, par_graph->ivps[k].idx, par_graph->ivps[k].val) ; k++ ;fprintf(stderr, "graph %s top=%d k=%d\n", allow_graph_ops ? "exec" : "skip", (int) offset, (int) k) ; } offset = top+1 ; } return mclxNrofEntries(mx) ; }
void test_for_cycles ( mclx* mx ) { mclx* tp = mclxTranspose(mx) ; mclv* fwd = mclxColSizes(mx, MCL_VECTOR_COMPLETE) ; mclv* bwd = mclxColSizes(tp, MCL_VECTOR_COMPLETE) ; dim i, n_cycle = 0 ; for (i=0;i<bwd->n_ivps;i++) { ofs level_up = fire_node(mx, i, NULL) ; ofs level_dn = fire_node(tp, i, NULL) ; if (level_up < 0 || level_dn < 0) fprintf(stderr, " [%lu cycle]", (ulong) i) , n_cycle++ ; } if (n_cycle) fputc('\n', stderr) ; mclvFree(&bwd) ; mclvFree(&fwd) ; mclxFree(&tp) ; fprintf ( stderr , "file with %lu edges has %d cycles\n" , (ulong) mclxNrofEntries(mx) , (int) n_cycle ) ; exit(n_cycle ? 1 : 0) ; }
mclMatrix* mclDag ( const mclMatrix* A , const mclInterpretParam* ipp ) { dim d ; double w_selfval= ipp ? ipp->w_selfval: 0.999 ; double w_maxval = ipp ? ipp->w_maxval : 0.001 ; double delta = ipp ? ipp->delta : 0.01 ; mclMatrix* M = mclxAllocZero ( mclvCopy(NULL, A->dom_cols) , mclvCopy(NULL, A->dom_rows) ) ; for (d=0; d<N_COLS(A); d++) /* thorough clean-up */ { mclVector* vec = A->cols+d ; mclVector* dst = M->cols+d ; double selfval = mclvIdxVal(vec, vec->vid, NULL) ; double maxval = mclvMaxValue(vec) ; double bar = selfval < maxval ? ( (w_selfval * selfval) + (w_maxval * maxval) ) : delta ? selfval / (1 + delta) : selfval ; int n_bar = mclvCountGiven(vec, mclpGivenValGQ, &bar) ; mclvCopyGiven(dst, vec, mclpGivenValGQ, &bar, n_bar) ; } if (0) { dim ne = mclxNrofEntries(M) ; fprintf(stderr, "nroff entries %u\n", (unsigned) ne) ; } return M ; }
mclx* handle_query ( mclx* mx , mcxIO* xfmx , mcxTing* sa , mcxTing* sb ) { if (!strcmp(sa->str, ":top")) handle_top(mx, sb) ; else if (!strcmp(sa->str, ":list")) handle_list(mx, sb) ; else if (!strcmp(sa->str, ":reread")) { mclxFree(&mx) ; if (xfabc_g) { streamer_g.tab_sym_in = tab_g ; mx = mclxIOstreamIn ( xfabc_g , MCLXIO_STREAM_ABC | (input_status != 'd' ? MCLXIO_STREAM_MIRROR : 0) | MCLXIO_STREAM_SYMMETRIC | MCLXIO_STREAM_GTAB_RESTRICT /* docme/fixme need to check for tab_g ? */ , NULL , mclpMergeMax , &streamer_g /* has tab, if present */ , EXIT_ON_FAIL ) ; mcxIOclose(xfabc_g) ; } else { mx = mclxReadx (xfmx, EXIT_ON_FAIL, MCLX_REQUIRE_GRAPH | MCLX_REQUIRE_CANONICAL) ; mcxIOclose(xfmx) ; } mclxAdjustLoops(mx, mclxLoopCBremove, NULL) ; } else if (!strcmp(sa->str, ":clcf")) handle_clcf(mx, sb) ; else if (!strcmp(sa->str, ":tf")) { handle_tf(mx, sb) ; mcxTell(me, "graph now has %lu arcs", (ulong) mclxNrofEntries(mx)) ; } else fprintf(stderr, "(error unknown-query (:clcf#1 :list#1 :reread :top#1))\n") ; return mx ; }
static void vary_threshold ( mcxIO* xf , FILE* fp , int vary_a , int vary_z , int vary_s , int vary_n , unsigned mode ) { dim cor_i = 0, j ; int step ; mclx* mx ; unsigned long noe ; pval* allvals ; dim n_allvals = 0 ; double sum_vals = 0.0 ; mx = mclxRead(xf, EXIT_ON_FAIL) ; mcxIOclose(xf) ; if (transform) mclgTFexec(mx, transform) ; noe = mclxNrofEntries(mx) ; allvals = mcxAlloc(noe * sizeof allvals[0], EXIT_ON_FAIL) ; if (!weight_scale) { if (mode == 'c') weight_scale = 1.0 ; else weight_scale = vary_n ; } n_allvals = get_n_sort_allvals(mx, allvals, noe, &sum_vals, FALSE) ; if (mode == 'c') { double smallest = n_allvals ? allvals[n_allvals-1] : -DBL_MAX ; if (vary_a * 1.0 / vary_n < smallest) { while (vary_a * 1.0 / vary_n < smallest) vary_a++ ; vary_a-- ; } mcxTell ( me , "smallest correlation is %.2f, using starting point %.2f" , smallest , vary_a * 1.0 / vary_n ) ; } if (output_flags & OUTPUT_TABLE) { ;fprintf(fp, "L\tD\tR\tS\tcce\tEWmean\tEWmed\tEWiqr\tNDmean\tNDmed\tNDiqr\tCCF\t%s\n", mode == 'k' ? "kNN" : mode == 'l' ? "N" : "Cutoff") ;} else { if (output_flags & OUTPUT_KEY) { ;fprintf(fp, "-------------------------------------------------------------------------------\n") ;fprintf(fp, " L Percentage of nodes in the largest component\n") ;fprintf(fp, " D Percentage of nodes in components of size at most %d [-div option]\n", (int) divide_g) ;fprintf(fp, " R Percentage of nodes not in L or D: 100 - L -D\n") ;fprintf(fp, " S Percentage of nodes that are singletons\n") ;fprintf(fp, " cce Expected size of component, nodewise [ sum(sz^2) / sum^2(sz) ]\n") ;fprintf(fp, "*EW Edge weight traits (mean, median and IQR, all scaled!)\n") ;fprintf(fp, " Scaling is used to avoid printing of fractional parts throughout.\n") ;fprintf(fp, " The scaling factor is %.2f [-report-scale option]\n", weight_scale) ;fprintf(fp, " ND Node degree traits [mean, median and IQR]\n") ;fprintf(fp, " CCF Clustering coefficient %s\n", compute_flags & COMPUTE_CLCF ? "(not computed; use --clcf to include this)" : "") ;fprintf(fp, " eff Induced component efficiency %s\n", compute_flags & COMPUTE_EFF ? "(not computed; use --eff to include this)" : "") ;if (mode == 'c') fprintf(fp, "Cutoff The threshold used.\n") ;else if (mode == 't') fprintf(fp, "*Cutoff The threshold with scale factor %.2f and fractional parts removed\n", weight_scale) ;else if (mode == 'k') fprintf(fp, "k-NN The knn parameter\n") ;else if (mode == 'l') fprintf(fp, "N The knn parameter (merge mode)\n") ;else if (mode == 'n') fprintf(fp, "ceil The ceil parameter\n") ;fprintf(fp, "Total number of nodes: %lu\n", (ulong) N_COLS(mx)) ;} fprintf(fp, "-------------------------------------------------------------------------------\n") ;fprintf(fp, " L D R S cce *EWmean *EWmed *EWiqr NDmean NDmed NDiqr CCF eff %6s \n", mode == 'k' ? "k-NN" : mode == 'l' ? "N" : mode == 'n' ? "Ceil" : "Cutoff") ;fprintf(fp, "-------------------------------------------------------------------------------\n") ; } for (step = vary_a; step <= vary_z; step += vary_s) { double cutoff = step * 1.0 / vary_n ; double eff = -1.0 ; mclv* nnodes = mclvCanonical(NULL, N_COLS(mx), 0.0) ; mclv* degree = mclvCanonical(NULL, N_COLS(mx), 0.0) ; dim i, n_sample = 0 ; double cor, y_prev, iqr = 0.0 ; mclx* cc = NULL, *res = NULL ; mclv* sz, *ccsz = NULL ; int step2 = vary_z + vary_a - step ; sum_vals = 0.0 ; if (mode == 't' || mode == 'c') mclxSelectValues(mx, &cutoff, NULL, MCLX_EQT_GQ) , res = mx ; else if (mode == 'k') { res = rebase_g ? mclxCopy(mx) : mx ; mclxKNNdispatch(res, step2, n_thread_l, 1) ; } else if (mode == 'l') { res = mx ; mclxKNNdispatch(res, step2, n_thread_l, 0) ; } else if (mode == 'n') { res = rebase_g ? mclxCopy(mx) : mx ; mclv* cv = mclgCeilNB(res, step2, NULL, NULL, NULL) ; mclvFree(&cv) ; } sz = mclxColSizes(res, MCL_VECTOR_COMPLETE) ; mclvSortDescVal(sz) ; cc = clmUGraphComponents(res, NULL) /* fixme: user has to specify -tf '#max()' if graph is directed */ ; if (cc) { ccsz = mclxColSizes(cc, MCL_VECTOR_COMPLETE) ; if (compute_flags & COMPUTE_EFF) { clmPerformanceTable pftable ; clmPerformance(mx, cc, &pftable) ; eff = pftable.efficiency ; } } if (mode == 't' || mode == 'c') { for ( ; n_allvals > 0 && allvals[n_allvals-1] < cutoff ; n_allvals-- ) ; sum_vals = 0.0 ; for (i=0;i<n_allvals;i++) sum_vals += allvals[i] ; } else if (mode == 'k' || mode == 'n' || mode == 'l') { n_allvals = get_n_sort_allvals(res, allvals, noe, &sum_vals, FALSE) ; } levels[cor_i].sim_median= mcxMedian(allvals, n_allvals, sizeof allvals[0], pval_get_double, &iqr) ; levels[cor_i].sim_iqr = iqr ; levels[cor_i].sim_mean = n_allvals ? sum_vals / n_allvals : 0.0 ; levels[cor_i].nb_median = mcxMedian(sz->ivps, sz->n_ivps, sizeof sz->ivps[0], ivp_get_double, &iqr) ; levels[cor_i].nb_iqr = iqr ; levels[cor_i].nb_mean = mclvSum(sz) / N_COLS(res) ; levels[cor_i].cc_exp = cc ? mclvPowSum(ccsz, 2.0) / N_COLS(res) : 0 ; levels[cor_i].nb_sum = mclxNrofEntries(res) ; if (compute_flags & COMPUTE_CLCF) { mclv* clcf = mclgCLCFdispatch(res, n_thread_l) ; levels[cor_i].clcf = mclvSum(clcf) / N_COLS(mx) ; mclvFree(&clcf) ; } else levels[cor_i].clcf = 0.0 ; levels[cor_i].threshold = mode == 'k' || mode == 'l' || mode == 'n' ? step2 : cutoff ; levels[cor_i].bigsize = cc ? cc->cols[0].n_ivps : 0 ; levels[cor_i].n_single = 0 ; levels[cor_i].n_edge = n_allvals ; levels[cor_i].n_lq = 0 ; if (cc) for (i=0;i<N_COLS(cc);i++) { dim n = cc->cols[N_COLS(cc)-1-i].n_ivps ; if (n == 1) levels[cor_i].n_single++ ; if (n <= divide_g) levels[cor_i].n_lq += n ; else break ; } if (levels[cor_i].bigsize <= divide_g) levels[cor_i].bigsize = 0 ; y_prev = sz->ivps[0].val /* wiki says: A scale-free network is a network whose degree distribution follows a power law, at least asymptotically. That is, the fraction P(k) of nodes in the network having k connections to other nodes goes for large values of k as P(k) ~ k^−g where g is a constant whose value is typically in the range 2<g<3, although occasionally it may lie outside these bounds. */ ; for (i=1;i<sz->n_ivps;i++) { double y = sz->ivps[i].val ; if (y > y_prev - 0.5) continue /* same as node degree seen last */ ; nnodes->ivps[n_sample].val = log( (i*1.0) / (1.0*N_COLS(res))) /* x = #nodes >= k, as fraction */ ; degree->ivps[n_sample].val = log(y_prev ? y_prev : 1) /* y = k = degree of node */ ; n_sample++ ;if(0)fprintf(stderr, "k=%.0f\tn=%d\t%.3f\t%.3f\n", (double) y_prev, (int) i, (double) nnodes->ivps[n_sample-1].val, (double) degree->ivps[n_sample-1].val) ; y_prev = y ; } nnodes->ivps[n_sample].val = 0 ; nnodes->ivps[n_sample++].val = log(y_prev ? y_prev : 1) ;if(0){fprintf(stderr, "k=%.0f\tn=%d\t%.3f\t%.3f\n", (double) sz->ivps[sz->n_ivps-1].val, (int) N_COLS(res), (double) nnodes->ivps[n_sample-1].val, (double) degree->ivps[n_sample-1].val) ;} ; mclvResize(nnodes, n_sample) ; mclvResize(degree, n_sample) ; cor = pearson(nnodes, degree, n_sample) ; levels[cor_i].degree_cor = cor * cor ;if(0)fprintf(stdout, "cor at cutoff %.2f %.3f\n\n", cutoff, levels[cor_i-1].degree_cor) ; mclvFree(&nnodes) ; mclvFree(°ree) ; mclvFree(&sz) ; mclvFree(&ccsz) ; mclxFree(&cc) ; if(output_flags & OUTPUT_TABLE) { fprintf ( fp , "%lu\t%lu\t%lu\t%lu\t%lu" "\t%6g\t%6g\t%6g" "\t%6g\t%lu\t%6g" , (ulong) levels[cor_i].bigsize , (ulong) levels[cor_i].n_lq , (ulong) N_COLS(mx) - levels[cor_i].bigsize - levels[cor_i].n_lq , (ulong) levels[cor_i].n_single , (ulong) levels[cor_i].cc_exp , (double) levels[cor_i].sim_mean , (double) levels[cor_i].sim_median , (double) levels[cor_i].sim_iqr , (double) levels[cor_i].nb_mean , (ulong) levels[cor_i].nb_median , (double) levels[cor_i].nb_iqr ) ; if (compute_flags & COMPUTE_CLCF) fprintf(fp, "\t%6g", levels[cor_i].clcf) ; else fputs("\tNA", fp) ; if (eff >= 0.0) fprintf(fp, "\t%4g", eff) ; else fputs("\tNA", fp) ; fprintf(fp, "\t%6g", (double) levels[cor_i].threshold) ; fputc('\n', fp) ; } else { fprintf ( fp , "%3d %3d %3d %3d %7d " "%7.0f %7.0f %6.0f" "%6.1f %6.0f %6.0f" , 0 ? 1 : (int) (0.5 + (100.0 * levels[cor_i].bigsize) / N_COLS(mx)) , 0 ? 1 : (int) (0.5 + (100.0 * levels[cor_i].n_lq) / N_COLS(mx)) , 0 ? 1 : (int) (0.5 + (100.0 * (N_COLS(mx) - levels[cor_i].bigsize - levels[cor_i].n_lq)) / N_COLS(mx)) , 0 ? 1 : (int) (0.5 + (100.0 * levels[cor_i].n_single) / N_COLS(mx)) , 0 ? 1 : (int) (0.5 + levels[cor_i].cc_exp) , 0 ? 1.0 : (double) (levels[cor_i].sim_mean * weight_scale) , 0 ? 1.0 : (double) (levels[cor_i].sim_median * weight_scale) , 0 ? 1.0 : (double) (levels[cor_i].sim_iqr * weight_scale) , 0 ? 1.0 : (double) (levels[cor_i].nb_mean ) , 0 ? 1.0 : (double) (levels[cor_i].nb_median + 0.5 ) , 0 ? 1.0 : (double) (levels[cor_i].nb_iqr + 0.5 ) ) ; if (compute_flags & COMPUTE_CLCF) fprintf(fp, " %3d", 0 ? 1 : (int) (0.5 + (100.0 * levels[cor_i].clcf))) ; else fputs(" -", fp) ; if (eff >= 0.0) fprintf(fp, " %3d", (int) (0.5 + 1000 * eff)) ; else fputs(" -", fp) ; if (mode == 'c') fprintf(fp, "%8.2f\n", (double) levels[cor_i].threshold) ; else if (mode == 't') fprintf(fp, "%8.0f\n", (double) levels[cor_i].threshold * weight_scale) ; else if (mode == 'k' || mode == 'n' || mode == 'l') fprintf(fp, "%8.0f\n", (double) levels[cor_i].threshold) ; } ; cor_i++ ; if (res != mx) mclxFree(&res) ; } if (!(output_flags & OUTPUT_TABLE)) { if (weefreemen) { fprintf(fp, "-------------------------------------------------------------------------------\n") ;fprintf(fp, "The graph below plots the R^2 squared value for the fit of a log-log plot of\n") ;fprintf(fp, "<node degree k> versus <#nodes with degree >= k>, for the network resulting\n") ;fprintf(fp, "from applying a particular %s cutoff.\n", mode == 'c' ? "correlation" : "similarity") ;fprintf(fp, "-------------------------------------------------------------------------------\n") ; for (j=0;j<cor_i;j++) { dim jj ; for (jj=30;jj<=100;jj++) { char c = ' ' ; if (jj * 0.01 < levels[j].degree_cor && (jj+1.0) * 0.01 > levels[j].degree_cor) c = 'X' ; else if (jj % 5 == 0) c = '|' ; fputc(c, fp) ; } if (mode == 'c') fprintf(fp, "%8.2f\n", (double) levels[j].threshold) ; else fprintf(fp, "%8.0f\n", (double) levels[j].threshold * weight_scale) ; } fprintf(fp, "|----+----|----+----|----+----|----+----|----+----|----+----|----+----|--------\n") ;fprintf(fp, "| R^2 0.4 0.5 0.6 0.7 0.8 0.9 | 1.0 -o)\n") ;fprintf(fp, "+----+----+----+----+----+---------+----+----+----+----+----+----+----+ /\\\\\n") ;fprintf(fp, "| 2 4 6 8 2 4 6 8 | 2 4 6 8 | 2 4 6 8 | 2 4 6 8 | 2 4 6 8 | 2 4 6 8 | _\\_/\n") ;fprintf(fp, "+----+----|----+----|----+----|----+----|----+----|----+----|----+----+--------\n") ; } else fprintf(fp, "-------------------------------------------------------------------------------\n") ; } mclxFree(&mx) ; mcxFree(allvals) ; }
int main ( int argc , const char* argv[] ) { mcxIO* xfmx = mcxIOnew("-", "r"), *xfout = mcxIOnew("-", "w") ; mclx* mx = NULL ; mclv* mx_diag = NULL ; mcxstatus parseStatus = STATUS_OK ; mcxOption* opts, *opt ; dim N_edge = 0 ; dim* offsets ; dim template_n_nodes = 0 ; mcxbool plus = FALSE ; double e_min = 1.0 ; double e_max = 0.0 ; double skew = 0.0 ; double radius = 0.0 ; double n_sdev = 0.5 ; double n_range = 2.0 ; double g_radius = 0.0 ; double g_mean = 0.0 ; double g_sdev = 0.0 ; double g_min = 1.0 ; double g_max = 0.0 ; mcxbool do_gaussian = FALSE ; dim i = 0 ; dim N_remove = 0 ; dim N_add = 0 ; dim N_shuffle = 0 ; unsigned long random_ignore = 0 ; srandom(mcxSeed(2308947)) ; mcxOptAnchorSortById(options, sizeof(options)/sizeof(mcxOptAnchor) -1) ; if (!(opts = mcxOptParse(options, (char**) argv, argc, 1, 0, &parseStatus))) exit(0) ; mcxLogLevel = MCX_LOG_AGGR | MCX_LOG_MODULE | MCX_LOG_IO | MCX_LOG_GAUGE | MCX_LOG_WARN ; mclxIOsetQMode("MCLXIOVERBOSITY", MCL_APP_VB_YES) ; mclx_app_init(stderr) ; for (opt=opts;opt->anch;opt++) { mcxOptAnchor* anch = opt->anch ; switch(anch->id) { case MY_OPT_HELP : case MY_OPT_APROPOS : mcxOptApropos(stdout, me, syntax, 20, MCX_OPT_DISPLAY_SKIP, options) ; return 0 ; case MY_OPT_VERSION : app_report_version(me) ; return 0 ; case MY_OPT_SKEW : skew = atof(opt->val) ; break ; case MY_OPT_GEN : template_n_nodes = atoi(opt->val) ; break ; case MY_OPT_IMX : mcxIOrenew(xfmx, opt->val, NULL) ; break ; case MY_OPT_PLUS : case MY_OPT_WB : plus = TRUE ; break ; case MY_OPT_OUT : mcxIOrenew(xfout, opt->val, NULL) ; break ; case MY_OPT_E_MAX : if (!strcmp(opt->val, "copy")) e_max = -DBL_MAX ; else e_max = atof(opt->val) ; break ; case MY_OPT_E_MIN : e_min = atof(opt->val) ; break ; case MY_OPT_G_MIN : g_min = atof(opt->val) ; break ; case MY_OPT_G_MAX : g_max = atof(opt->val) ; break ; case MY_OPT_G_SDEV : g_sdev = atof(opt->val) ; break ; case MY_OPT_G_MEAN : g_mean = atof(opt->val) ; do_gaussian = TRUE ; break ; case MY_OPT_G_RADIUS : g_radius = atof(opt->val) ; break ; case MY_OPT_N_RANGE : n_range = atof(opt->val) ; break ; case MY_OPT_N_SDEV : n_sdev = atof(opt->val) ; break ; case MY_OPT_N_RADIUS : radius = atof(opt->val) ; break ; case MY_OPT_SHUFFLE : N_shuffle = atoi(opt->val) ; break ; case MY_OPT_ADD : N_add = atoi(opt->val) ; break ; case MY_OPT_REMOVE : N_remove = atoi(opt->val) ; break ; } } /* hitting y% in vi tells me the size of this block */ { if (template_n_nodes) mx = mclxAllocZero ( mclvCanonical(NULL, template_n_nodes, 1.0) , mclvCanonical(NULL, template_n_nodes, 1.0) ) ; else mx = mclxReadx ( xfmx , EXIT_ON_FAIL , MCLX_REQUIRE_GRAPH ) ; mx_diag = mclxDiagValues(mx, MCL_VECTOR_COMPLETE) ; if (N_shuffle) mclxAdjustLoops(mx, mclxLoopCBremove, NULL) ; else mclxSelectUpper(mx) /* ^ apparently we always work on single arc representation (docme andsoon) */ ; offsets = mcxAlloc(sizeof offsets[0] * N_COLS(mx), EXIT_ON_FAIL) ; N_edge = 0 ; for (i=0;i<N_COLS(mx);i++) { offsets[i] = N_edge ; N_edge += mx->cols[i].n_ivps ; } if (N_edge < N_remove) { mcxErr ( me , "removal count %ld exceeds edge count %ld" , (long) N_remove , (long) N_edge ) ; N_remove = N_edge ; } random_ignore = RAND_MAX - (N_edge ? RAND_MAX % N_edge : 0) ; if (RAND_MAX / 2 < N_edge) mcxDie(1, me, "graph too large!") ; if (N_shuffle) { do_the_shuffle(mx, N_shuffle, offsets, N_edge, random_ignore) ; mx_readd_diagonal(mx, mx_diag) ; mclxWrite(mx, xfout, MCLXIO_VALUE_GETENV, RETURN_ON_FAIL) ; exit(0) ; } ; if (N_remove) { dim n_remove = do_remove(mx, N_remove, offsets, N_edge, random_ignore) /* Need to recompute N_edge and random_ignore. * NOTE we work with *upper* matrix; this counts graph edges. */ ; N_edge = mclxNrofEntries(mx) - n_remove ; random_ignore = RAND_MAX - (RAND_MAX % N_COLS(mx)) ; } if (g_mean) { if (!g_radius) { if (g_sdev) g_radius = 2 * g_sdev ; mcxWarn(me, "set radius to %.5f\n", g_radius) ; } } ; if (N_add) N_edge += do_add ( mx , N_add , N_edge , do_gaussian ? &g_mean : NULL, g_radius , g_sdev , g_min , g_max , skew , e_min , e_max ) ; if (radius) { for (i=0;i<N_COLS(mx);i++) { mclp* ivp = mx->cols[i].ivps, *ivpmax = ivp + mx->cols[i].n_ivps ;if(DEBUG)fprintf(stderr, "here %d\n", (int) i) ; while (ivp < ivpmax) { double val = ivp->val ; double r = mcxNormalCut(n_range * n_sdev, n_sdev) ; double newval = val + radius * (r / (n_range * n_sdev)) ; if (e_min < e_max && newval >= e_min && newval <= e_max) ; ivp->val = newval ; ivp++ ; } } } mclxUnary(mx, fltxCopy, NULL) /* remove zeroes */ ; mclxAddTranspose(mx, 0.0) ; mx_readd_diagonal(mx, mx_diag) ; if (plus) mclxbWrite(mx, xfout, RETURN_ON_FAIL) ; else mclxWrite(mx, xfout, MCLXIO_VALUE_GETENV, RETURN_ON_FAIL) ; } return 0 ; }
int main ( int argc , const char* argv[] ) { mcxIO *xfcl = NULL , *xfctrl = NULL , *xfcoarse= NULL , *xfbase = NULL , *xfcone = NULL , *xfstack = NULL ; mclx* mxbase, *cl, *cl_coarse, *clprev, *clctrl = NULL ; mcxTing* shared = mcxTingNew("-I 4 -overlap split") ; mcxbool root = TRUE ; mcxbool have_bootstrap = FALSE ; const char* plexprefix = NULL ; const char* stem = "mcl" ; mcxbool same = FALSE ; mcxbool plex = TRUE ; mcxbool add_transpose = FALSE ; const char* b2opts = NULL ; const char* b1opts = NULL ; mcxbits write_modes = 0 ; mclAlgParam* mlp = NULL ; mcxstatus status = STATUS_OK ; mcxstatus parse_status = STATUS_OK ; int multiplex_idx = 1 ; int N = 0 ; int n_ite = 0 ; dim n_components = 0, n_cls = 0 ; int a = 1, i= 0 ; int n_arg_read = 0 ; int delta = 0 ; mcxOption* opts, *opt ; mcxTing* cline = mcxOptArgLine(argv+1, argc-1, '\'') ; mclgTF* transform = NULL ; mcxTing* transform_spec = NULL ; double iaf = 0.84 ; mclx_app_init(stderr) ; if (0) mcxLogLevel = MCX_LOG_AGGR | MCX_LOG_MODULE | MCX_LOG_IO | MCX_LOG_GAUGE | MCX_LOG_WARN ; else mcxLogLevelSetByString("xf4g1") ; mcxOptAnchorSortById(options, sizeof(options)/sizeof(mcxOptAnchor) -1) ; if (argc == 2 && argv[1][0] == '-' && mcxOptIsInfo(argv[1], options)) delta = 1 ; else if (argc < 2) { help(options, shared) ; exit(0) ; } opts = mcxOptExhaust (options, (char**) argv, argc, 2-delta, &n_arg_read, &parse_status) ; if (parse_status != STATUS_OK) { mcxErr(me, "initialization failed") ; exit(1) ; } ; for (opt=opts;opt->anch;opt++) { mcxOptAnchor* anch = opt->anch ; switch(anch->id) { case MY_OPT_HELP : help(options, shared) ; exit(0) ; case MY_OPT_APROPOS : help(options, shared) ; exit(0) ; break ; case MY_OPT_NMAX : N = atoi(opt->val) ; break ; case MY_OPT_Z : help(NULL, shared) ; exit(0) ; break ; case MY_OPT_SHARED : mcxTingPrintAfter(shared, " %s", opt->val) ; break ; case MY_OPT_TRANSFORM : transform_spec = mcxTingNew(opt->val) ; break ; case MY_OPT_B1 : b1opts = opt->val ; break ; case MY_OPT_B2 : b2opts = opt->val ; break ; case ALG_OPT_SETENV : mcxSetenv(opt->val) ; break ; case ALG_OPT_QUIET : mcxLogLevelSetByString(opt->val) ; break ; case MY_OPT_HDP : hdp_g = atof(opt->val) ; break ; case MY_OPT_ADDTP : add_transpose = TRUE ; break ; case MY_OPT_ANNOT /* only used in command-line copying */ : break ; case MY_OPT_IAF : iaf = atof(opt->val) / 100 ; break ; case MY_OPT_WRITE : if (strstr(opt->val, "stack")) write_modes |= OUTPUT_STACK ; if (strstr(opt->val, "cone")) write_modes |= OUTPUT_CONE ; if (strstr(opt->val, "levels")) write_modes |= OUTPUT_STEPS ; if (strstr(opt->val, "coarse")) write_modes |= OUTPUT_COARSE ; if (strstr(opt->val, "base")) write_modes |= OUTPUT_BASE ; break ; case MY_OPT_BASENAME : xfbase = mcxIOnew(opt->val, "w") ; break ; case MY_OPT_COARSE : xfcoarse = mcxIOnew(opt->val, "w") ; break ; case MY_OPT_CONE : xfcone = mcxIOnew(opt->val, "w") ; break ; case MY_OPT_ROOT : root = strchr("1yY", (u8) opt->val[0]) ? TRUE : FALSE ; break ; case MY_OPT_STACK : xfstack = mcxIOnew(opt->val, "w") ; break ; case MY_OPT_STEM : stem = opt->val ; break ; case MY_OPT_MULTIPLEX : plex = strchr("yY1", (unsigned char) opt->val[0]) ? TRUE : FALSE ; break ; case MY_OPT_DISPATCH : dispatch_g = TRUE ; break ; case MY_OPT_INTEGRATE : integrate_g = TRUE ; break ; case MY_OPT_CONTRACT : break ; case MY_OPT_SUBCLUSTERX : subclusterx_g = TRUE, subcluster_g = TRUE ; break ; case MY_OPT_SUBCLUSTER : subcluster_g = TRUE ; break ; case MY_OPT_CONTROL : xfctrl = mcxIOnew(opt->val, "r") ; break ; case MY_OPT_CL : xfcl = mcxIOnew(opt->val, "r") ; have_bootstrap = TRUE ; break ; case MY_OPT_VERSION : app_report_version(me) ; exit(0) ; default : mcxExit(1) ; } } mcxOptFree(&opts) ; a = 2 + n_arg_read ; if (a < argc) { if (strcmp(argv[a], "--")) mcxDie ( 1 , me , "trailing %s options require standalone '--' separator (found %s)" , integrate_g ? "integrate" : "mcl" , argv[a] ) ; a++ ; } if (subcluster_g + dispatch_g + integrate_g > 1) mcxDie(1, me, "too many modes!") ; if (N && N < argc-a) mcxErr(me, "-n argument leaves spurious option specifications") ; srandom(mcxSeed(89315)) ; signal(SIGALRM, mclSigCatch) ; if (dispatch_g) plexprefix = "dis" ; else if (!write_modes || (write_modes & OUTPUT_STEPS)) plexprefix = stem ; { mcxTing* tg = mcxTingEmpty(NULL, 30) ; if ((write_modes & OUTPUT_COARSE) && !xfcoarse) mcxTingPrint(tg, "%s.%s", stem, "coarse") , xfcoarse = mcxIOnew(tg->str, "w") ; if ((write_modes & OUTPUT_BASE) && !xfbase) mcxTingPrint(tg, "%s.%s", stem, "base") , xfbase = mcxIOnew(tg->str, "w") ; if ( (!write_modes || (write_modes & OUTPUT_CONE)) && !xfcone ) { mcxTingPrint(tg, "%s.%s", stem, "cone") ; xfcone = mcxIOnew(tg->str, "w") ; mcxIOopen(xfcone, EXIT_ON_FAIL) ; fprintf(xfcone->fp, "# %s %s\n", argv[0], cline->str) ; } if ((write_modes & OUTPUT_STACK) && !xfstack) { mcxTingPrint(tg, "%s.%s", stem, "stack") ; xfstack = mcxIOnew(tg->str, "w") ; mcxIOopen(xfstack, EXIT_ON_FAIL) ; fprintf(xfstack->fp, "# %s %s\n", argv[0], cline->str) ; } mcxTingFree(&tg) ; } if (integrate_g) { for (i=a;i<argc;i++) { mcxIO* xf = mcxIOnew(argv[i], "r") ; mclx* cl = mclxRead(xf, EXIT_ON_FAIL) ; mclxCatPush(&stck_g, cl, NULL, NULL, mclxCBdomStack, NULL, "dummy-integrate", n_cls++) ; } integrate_results(&stck_g) ; if (xfstack) mclxCatWrite(xfstack, &stck_g, MCLXIO_VALUE_NONE, RETURN_ON_FAIL) ; if (xfcone) mclxCatConify(&stck_g) , mclxCatWrite(xfcone, &stck_g, MCLXIO_VALUE_NONE, RETURN_ON_FAIL) ; return 0 ; } for (i=a;i<argc;i++) { if (get_interface(NULL, argv[1], shared->str, argv[i], NULL, 0, RETURN_ON_FAIL)) mcxDie(1, me, "error while testing mcl options viability (%s)", argv[i]) ; } mcxLog(MCX_LOG_APP, me, "pid %ld", (long) getpid()) /* make sure clusters align with this cluster * status: does not seem promising. */ ; if (xfctrl) clctrl = mclxRead(xfctrl, EXIT_ON_FAIL) ; /* * Below: compute cl and mxbase. */ ; if (xfcl) { cl = mclxRead(xfcl, EXIT_ON_FAIL) ; write_clustering (cl, NULL, xfcone, xfstack, plexprefix, multiplex_idx++, NULL) ; if (subcluster_g || dispatch_g) mclxCatPush(&stck_g, cl, NULL, NULL, mclxCBdomStack, NULL, "dummy-mclcm", n_cls++) ; mcxIOfree(&xfcl) ; if (!b1opts && !b2opts) b1opts = "" ; mxbase = get_base(argv[1], NULL, b1opts, b2opts) ; } else { mcxbits CACHE = b1opts || b2opts ? ALG_CACHE_INPUT /* cache, transform later */ : ALG_CACHE_START ; get_interface ( &mlp , argv[1] , shared->str , a < argc ? argv[a] : NULL , NULL , CACHE , EXIT_ON_FAIL ) ; if (a < argc) a++ ; if ((status = mclAlgorithm(mlp)) == STATUS_FAIL) { mcxErr(me, "failed at initial run") ; exit(1) ; } cl_coarse = mclAlgParamRelease(mlp, mlp->cl_result) ; cl_coarse = control_test(cl_coarse, clctrl) ; write_clustering (cl_coarse, NULL, xfcone, xfstack, plexprefix, multiplex_idx++, mlp) ; if (subcluster_g || dispatch_g) mclxCatPush(&stck_g, cl_coarse, NULL, NULL, mclxCBdomStack, NULL, "dummy-mclcm", n_cls++) ; cl = cl_coarse ; n_ite++ ; if (b1opts || b2opts) { mclx* mx_input = mclAlgParamRelease(mlp, mlp->mx_input) ; mxbase = get_base(NULL, mx_input, b1opts, b2opts) /* ^ get_base frees mx_input */ ; } else mxbase = mclAlgParamRelease(mlp, mlp->mx_start) ; } clprev = cl ; mclAlgParamFree(&mlp, TRUE) ; if (xfbase) { dim nre = mclxNrofEntries(mxbase) ; mcxLog(MCX_LOG_APP, me, "base has %lu entries", (ulong) nre) ; mclxaWrite(mxbase, xfbase, MCLXIO_VALUE_GETENV, EXIT_ON_FAIL) ; mcxIOclose(xfbase) ; } if (subcluster_g || dispatch_g) iaf = iaf ? 1/iaf : 1.414 ; while ( (!dispatch_g && (!N || n_ite < N)) || (dispatch_g && a < argc) ) { mclx* mx_coarse = NULL, *clnext = NULL ; dim dist_new_prev = 0, dist_prev_new = 0 ; mclx* clnew = NULL ; mcxbool faith = FALSE ; double inflation = -1.0 ; if (subcluster_g) mx_coarse = subclusterx_g ? mclxBlockPartition(mxbase, clprev, 50) : mclxBlockUnion(mxbase, clprev) /* have to copy mxbase as mx_coarse is freed. * Even if it were not freed, it is probably transformed. */ ; else if (dispatch_g) mx_coarse = mclxCopy(mxbase) ; else { mx_coarse = get_coarse(mxbase, clprev, add_transpose) ; if (n_ite == 1) { mclx* cc = clmUGraphComponents(mx_coarse, NULL) /* fixme; mx_coarse garantueed UD ? */ ; n_components = N_COLS(cc) ; mclxFree(&cc) ; } } if (xfcoarse) write_coarse(xfcoarse, mx_coarse) ; get_interface ( &mlp , NULL , shared->str , a < argc ? argv[a] : NULL , mx_coarse , ALG_CACHE_START , EXIT_ON_FAIL ) ; inflation = mlp->mpp->mainInflation ; BIT_OFF(mlp->modes, ALG_DO_SHOW_PID | ALG_DO_SHOW_JURY) ; if ((status = mclAlgorithm(mlp)) == STATUS_FAIL) { mcxErr(me, "failed") ; mcxExit(1) ; } cl_coarse = mclAlgParamRelease(mlp, mlp->cl_result) ; if (xfcoarse) mclxaWrite(cl_coarse, xfcoarse, MCLXIO_VALUE_NONE, RETURN_ON_FAIL) ; if (dispatch_g || subcluster_g) clnext = cl_coarse ; else clnext = mclxCompose(clprev, cl_coarse, 0) , clnext = control_test(clnext, clctrl) , mclxFree(&cl_coarse) ; clmSJDistance (clprev, clnext, NULL, NULL, &dist_prev_new, &dist_new_prev) ; if (dist_prev_new + dist_new_prev) { write_clustering (clnext, clprev, xfcone, xfstack, plexprefix, multiplex_idx++, mlp) ; clnew = clnext ; if (subcluster_g || dispatch_g) mclxCatPush(&stck_g, clnext, NULL, NULL, mclxCBdomStack, NULL, "dummy-mclcm", n_cls++) ; else mclxFree(&clprev) ; clprev = clnew ; } else if ( N_COLS(clnext) > n_components && inflation * iaf > 1.2 && inflation * iaf < 10 ) { mclxFree(&clnext) ; inflation *= iaf ; mcxTingPrintAfter(shared, " -I %.2f", inflation) ; mcxLog(MCX_LOG_APP, me, "setting inflation to %.2f", inflation) ; faith = TRUE ; } /* i.e. vanilla mode, contraction */ else if (!subcluster_g && !dispatch_g) { mclx* cc ; mclxFree(&clnext) ; mclxAddTranspose(mx_coarse, 1.0) ; cc = clmUGraphComponents(mx_coarse, NULL) ; if (N_COLS(cc) < N_COLS(clprev)) { mclx* ccback = mclxCompose(clprev, cc, 0) ; write_clustering (ccback, clprev, xfcone, xfstack, plexprefix, multiplex_idx++, NULL) ; mclxFree(&clprev) ; clprev = ccback ; mcxTell(me, "connected components added as root clustering") ; } if (root && N_COLS(cc) > 1) { mclx* root = mclxCartesian ( mclvCanonical(NULL, 1, 0) , mclvCopy(NULL, mxbase->dom_cols) , 1.0 ) ; write_clustering (root, clprev, xfcone, xfstack, plexprefix, multiplex_idx++, NULL) ; mclxFree(&clprev) ; mcxTell(me, "universe added as root clustering") ; clprev = root ; clnew = NULL ; } mclxFree(&cc) ; } else if (subcluster_g || dispatch_g) mclxFree(&clnext) ; mclAlgParamFree(&mlp, TRUE) /* frees mx_coarse */ ; if (!clnew && !faith) { same = TRUE ; break ; } a++ ; if (dispatch_g && a == argc) break ; n_ite++ ; } if (same) mcxLog(MCX_LOG_MODULE, me, "no further contraction: halting") ; if (dispatch_g) integrate_results(&stck_g) ; else if (subcluster_g) mclxCatReverse(&stck_g) ; if (dispatch_g || subcluster_g) { dim j ; if (xfstack) mclxCatWrite(xfstack, &stck_g, MCLXIO_VALUE_NONE, RETURN_ON_FAIL) ; if (xfcone && ! mclxCatConify(&stck_g)) mclxCatWrite(xfcone, &stck_g, MCLXIO_VALUE_NONE, RETURN_ON_FAIL) ; for (j=0;j<stck_g.n_level;j++) { mclxAnnot* an = stck_g.level+j ; mclxFree(&an->mx) ; } mcxFree(stck_g.level) ; } mcxIOfree(&xfcoarse) ; mcxIOfree(&xfbase) ; mcxIOfree(&xfcone) ; mcxIOfree(&xfstack) ; mcxTingFree(&shared) ; if (!dispatch_g && !subcluster_g) /* fixme fixme fixme */ mclxFree(&clprev) ; mclxFree(&mxbase) ; mclvFree(&start_col_sums_g) ; mcxTingFree(&cline) ; helpful_reminder() ; return STATUS_OK ; }