+++ /dev/null
-#include <spine/spinehdr.h>
-#include <spine/subset.h>
-#include <spine/quad.h>
-#include <spine/union_find.h>
-#include <assert.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <math.h>
-#ifdef MAIN
-#include <getopt.h>
-#include <ingraphs/ingraphs.h>
-
-typedef struct {
- FILE *outfp;
- char **Files;
- float sparse_ratio;
- int verbose;
-} opts_t;
-#endif
-
-typedef int (*qsort_cmpf) (const void *, const void *);
-
-#define MIN(a,b) ((a)<(b)?(a):(b))
-#define MAX(a,b) ((a)>(b)?(a):(b))
-
-void* mcalloc (size_t cnt, size_t sz)
-{
- void* p = calloc(cnt, sz);
- /* fprintf(stderr, "alloc %lu bytes %p\n", cnt*sz, p); */
- return p;
-}
-
-#if 0
-static float ewt(Agedge_t * e)
-{
- return ED_wt(e);
-}
-#endif
-
-static int cmpe(void *v0, void *v1)
-{
- Agedge_t *e0 = *(Agedge_t **) v0;
- Agedge_t *e1 = *(Agedge_t **) v1;
-
- if (ED_wt(e0) > ED_wt(e1))
- return -1;
- else if (ED_wt(e0) < ED_wt(e1))
- return 1;
- else
- return 0;
-}
-
-
-static void doEdge(Agraph_t * g, Agnode_t * v, Agnode_t * w, int *quadcnt)
-{
- Agedge_t *e = agedge(g, v, w, 0, 0);
- if (!e)
- e = agedge(g, w, v, 0, 0);
- if (!e) {
- fprintf(stderr, "Could not find edge %s--%s\n", agnameof(v),
- agnameof(w));
- exit(1);
- }
- quadcnt[ED_id(e)] += 1;
-}
-
-static void
-recordQuads(Agnode_t * v, Agnode_t * w, Dt_t * subset, void *state)
-{
- Dtlink_t *link0;
- Dtlink_t *link1;
- Agnode_t *u0;
- Agnode_t *u1;
- int *quadcnt = (int *) state;
- Agraph_t *g = agroot(v);
-
- for (link0 = dtflatten(subset); link0; link0 = dtlink(subset, link0)) {
- u0 = (Agnode_t *) (((ptritem *) dtobj(subset, link0))->v);
- for (link1 = dtlink(subset, link0); link1;
- link1 = dtlink(subset, link1)) {
- u1 = (Agnode_t *) (((ptritem *) dtobj(subset, link1))->v);
- doEdge(g, v, u0, quadcnt);
- doEdge(g, w, u0, quadcnt);
- doEdge(g, v, u1, quadcnt);
- doEdge(g, w, u1, quadcnt);
- }
- }
-}
-
-static void
-reweightEdge (Agedge_t* e, Dt_t* nbr0, Dt_t* nbr1, Agedge_t*** nbrs, int verbose)
-{
- Agnode_t* tail = agtail(e);
- Agnode_t* head = aghead(e);
- Agedge_t** tail_edgelist = nbrs[ND_id(tail)];
- long int len0 = nbrs[ND_id(tail)+1] - tail_edgelist;
- Agedge_t** head_edgelist = nbrs[ND_id(head)];
- long int len1 = nbrs[ND_id(head)+1] - head_edgelist;
- long int minlen = MIN(len0, len1);
- long int i;
- long int maxi = 0;
- double wt, maxwt = 0;
- double common_cnt = 0;
- double union_cnt = 0;
- Agnode_t* n0;
- Agnode_t* n1;
- double oldwt;
-
- clearSubset(nbr0);
- clearSubset(nbr1);
-
- if (verbose > 1)
- oldwt = ED_wt(e);
-
-#ifdef TEST_JACCARD
- Dt_t* nbr00 = mkSubset();
- Dt_t* nbr11 = mkSubset();
- double wt0;
-#endif
- for (i = 0; i < minlen; i++) {
- n0 = (*tail_edgelist++)->node;
- n1 = (*head_edgelist++)->node;
- assert(n0 != tail);
- assert(n1 != head);
-#ifdef TEST_JACCARD
- addSubset(nbr00, n0);
- addSubset(nbr11, n1);
-#endif
-/* fprintf (stderr, "add %s %s\n", agnameof(n0), agnameof(n1)); */
- if (n0 != n1) {
- if (inSubset(nbr1, n0)) common_cnt++;
- else {
- addSubset (nbr0, n0);
- union_cnt++;
- }
- if (inSubset(nbr0, n1)) common_cnt++;
- else {
- addSubset (nbr1, n1);
- union_cnt++;
- }
- }
- else {
- common_cnt++;
- union_cnt++;
- }
- wt = common_cnt/union_cnt;
-#ifdef TEST_JACCARD
- wt0 = ((double)intersect_size(nbr00,nbr11))/union_size(nbr00,nbr11);
- assert(wt == wt0);
-#endif
- if (wt > maxwt) {
- maxi = i;
- maxwt = wt;
- }
- }
- if (len0 > minlen) {
- for (; i < len0; i++) {
- n0 = (*tail_edgelist++)->node;
-/* fprintf (stderr, "add %s -\n", agnameof(n0)); */
-#ifdef TEST_JACCARD
- addSubset(nbr00, n0);
-#endif
- if (inSubset(nbr1, n0)) common_cnt++;
- else union_cnt++;
- wt = common_cnt/union_cnt;
-#ifdef TEST_JACCARD
- wt0 = ((double)intersect_size(nbr00,nbr11))/union_size(nbr00,nbr11);
- assert(wt == wt0);
-#endif
- if (wt > maxwt) {
- maxi = i;
- maxwt = wt;
- }
- }
- }
- else if (len1 > minlen) {
- for (; i < len1; i++) {
- n1 = (*head_edgelist++)->node;
-/* fprintf (stderr, "add - %s\n", agnameof(n1)); */
-#ifdef TEST_JACCARD
- addSubset(nbr11, n1);
-#endif
- if (inSubset(nbr0, n1)) common_cnt++;
- else union_cnt++;
- wt = common_cnt/union_cnt;
-#ifdef TEST_JACCARD
- wt0 = ((double)intersect_size(nbr00,nbr11))/union_size(nbr00,nbr11);
- assert(wt == wt0);
-#endif
- if (wt > maxwt) {
- maxi = i;
- maxwt = wt;
- }
- }
- }
-
- ED_wt(e) = maxwt;
- if (verbose > 1)
- fprintf(stderr, "%s : %s %f %ld/%ld %f\n",
- agnameof(tail), agnameof(head), maxwt, maxi, MAX(len0, len1), oldwt);
-#ifdef TEST_JACCARD
- closeSubset(nbr00);
- closeSubset(nbr11);
-#endif
-}
-
-static void setEdgeWeights(Agraph_t * g, int verbose)
-{
- int *quadcnt = N_NEW((size_t)agnedges(g), int);
- int ncnt = agnnodes(g);
- int *que = N_NEW((size_t)ncnt, int);
- Agnode_t *n;
- Agedge_t *e;
- int iwt;
- int edgecnt = 0;
- long int i = 0;
-
- /* Count the number q(u,v) of quadrilaterals each edge is in.
- * This is stored in quadcnt, indexed by the edges index.
- */
- genQuads(g, recordQuads, quadcnt);
-
- /* Weight node v by q(v), the sum of the q(u,v) for all neighbors v of u.
- * This is stored in que, indexed by the node's index.
- */
- for (n = agfstnode(g); n; n = agnxtnode(g, n)) {
- ND_id(n) = i++;
- iwt = 0;
- for (e = agfstout(g, n); e; e = agnxtout(g, e)) {
- iwt += quadcnt[ED_id(e)];
- edgecnt++;
- }
- for (e = agfstin(g, n); e; e = agnxtin(g, e)) {
- iwt += quadcnt[ED_id(e)];
- }
- que[ND_id(n)] = iwt;
-#if 0
- fprintf(stderr, " %s quad %d\n", agnameof(n), que[ND_id(n)]);
-#endif
- }
-
- /* Assign each edge a normalized initial weight Q(u,v) which is q(u,v)/sqrt(q(u)q(v)).
- * This is stored in ED_wt.
- */
- for (n = agfstnode(g); n; n = agnxtnode(g, n)) {
- for (e = agfstout(g, n); e; e = agnxtout(g, e)) {
- int quadv = quadcnt[ED_id(e)];
- if (quadv)
- ED_wt(e) =
- quadv /
- sqrt((double) (que[ND_id(n)] * que[ND_id(aghead(e))]));
- else
- ED_wt(e) = 0;
-#if 0
- fprintf(stderr, " %s--%s quadcnt %d wt %f\n",
- agnameof(n), agnameof(aghead(e)), quadcnt[ED_id(e)],
- jD_wt(e));
-#endif
- }
- }
-
- free(quadcnt);
- free(que);
-
- Agedge_t** edges = N_NEW((size_t)(2*edgecnt+1),Agedge_t*);
- Agedge_t*** nbrs = N_NEW((size_t)ncnt+1, Agedge_t**);
- Agedge_t** edgelist = edges;
- size_t degree;
- /* For each node, sort its edges by Q(u,v). */
- for (n = agfstnode(g); n; n = agnxtnode(g, n)) {
- degree = 0;
- nbrs[ND_id(n)] = edgelist;
- for (e = agfstout(g, n); e; e = agnxtout(g, e)) {
- degree++;
- *edgelist++ = e;
- }
- for (e = agfstin(g, n); e; e = agnxtin(g, e)) {
- degree++;
- *edgelist++ = e;
- }
- qsort(nbrs[ND_id(n)], degree, sizeof(Agedge_t **), (qsort_cmpf)cmpe);
-/*
- fprintf (stderr, "sort %s(%d) degree %lu %d %p\n",
- agnameof(n), ND_id(n), degree, agdegree(g,n,1,1), nbrs[ND_id(n)]);
-*/
- }
- nbrs[ncnt] = edgelist;
-
-#if 0
- for (n = agfstnode(g); n; n = agnxtnode(g, n)) {
- edgelist = nbrs[ND_id(n)];
- long int len0 = nbrs[ND_id(n)+1] - edgelist;
- fprintf (stderr, "%s len %lu degree %d\n", agnameof(n), len0, agdegree(g,n,1,1));
- for (i = 0; i < len0; i++) {
- e = *edgelist++;
- fprintf (stderr, "%s %s %lf\n",
- agnameof(agtail(e)), agnameof(aghead(e)), ED_wt(e));
- }
- }
-#endif
-
- /* Finally, for each edge (u,v), compute the Jaccard coefficient of the union of
- * k neighbors of u and v, using the sorted edges. The final edge weight is the
- * maximum Jaccard coefficient.
- */
- Dt_t* nbr0 = mkSubset();
- Dt_t* nbr1 = mkSubset();
- for (n = agfstnode(g); n; n = agnxtnode(g, n)) {
- edgelist = nbrs[ND_id(n)];
- long int len0 = nbrs[ND_id(n)+1] - edgelist;
- for (i = 0; i < len0; i++) {
- e = *edgelist++;
- if (AGTYPE(e)==AGINEDGE) continue;
- reweightEdge (e, nbr0, nbr1, nbrs, verbose);
- }
- }
- closeSubset(nbr0);
- closeSubset(nbr1);
- free(edges);
- free(nbrs);
-}
-
-/* Return number in range [0,nedges] */
-static size_t computeIndex(size_t nedges, float s)
-{
- size_t r = ceilf(nedges * (1 - s));
- return r;
-}
-
-static size_t doBucket(Agedge_t ** edgelist, size_t idx, Dt_t * M)
-{
- Agedge_t *e;
- float weight = ED_wt(edgelist[idx]);
-
- while ((e = edgelist[idx]) && (ED_wt(e) == weight)) {
- idx++;
- if (UF_find(agtail(e)) != UF_find(aghead(e)))
- addSubset(M, e);
- }
-
- return idx;
-}
-
-static int walker(Agedge_t * e, Agraph_t * sg)
-{
- UF_union(agtail(e), aghead(e));
- agsubedge(sg, e, 1);
- return 0;
-}
-
-static Agraph_t *findUMST(Agraph_t * g, Agedge_t ** edgelist, size_t nedges)
-{
- Agraph_t *sg = agsubg(g, "UMST", 1);
- Dt_t *M = mkSubset();
-
- size_t i = 0;
- while (i < nedges) {
- i = doBucket(edgelist, i, M);
- /* for each edge in M, add to sg, and union nodes */
- walkSubset(M, (walkfn) walker, sg);
- if (i < nedges)
- clearSubset(M);
- }
- closeSubset(M);
- return sg;
-}
-
-/* Remove loops and multiedges. */
-static void cleanGraph (Agraph_t * g, int verbose)
-{
- Agnode_t *n;
- Agnode_t *head;
- Agedge_t *e;
- Agedge_t *nexte;
- Agedge_t *inexte;
- Agedge_t *backe;
- Agedge_t *preve = NULL;
- int loopcnt = 0;
- int multicnt = 0;
- for (n = agfstnode(g); n; n = agnxtnode(g, n)) {
- preve = NULL;
- for (e = agfstout(g, n); e; e = nexte) {
- head = aghead(e);
- nexte = agnxtout(g, e);
- if (head == n) {
- agdelete(g, e);
- preve = NULL;
- loopcnt++;
- }
- else if (preve && (head == aghead(preve))) {
- agdelete(g, e);
- multicnt++;
- }
- else {
- preve = e;
- if ((backe = agedge(g, head, n, 0, 0))) {
- while (backe && (agtail(backe) == head)) {
- multicnt++;
- inexte = agnxtin(g, backe);
- agdelete(g, backe);
- backe = inexte;
- }
- }
-
- }
- }
- }
- if (verbose)
- fprintf (stderr, "cleanGraph: %d loops %d multiedges removed\n", loopcnt, multicnt);
-}
-
-void genSpine(Agraph_t * g, float sparse_ratio, int verbose)
-{
- Agraph_t *sg_union;
- Agnode_t *n;
- Agedge_t *e;
- Agedge_t **edgelist;
- size_t i, index;
- size_t nedges;
- float threshold;
-
- cleanGraph (g, verbose);
- nedges = agnedges(g);
- if (verbose)
- fprintf(stderr, "Graph %s %d nodes %lu edges:\n", agnameof(g),
- agnnodes(g), nedges);
- aginit(g, AGNODE, "nodeinfo", sizeof(nodeinfo_t), 1);
- aginit(g, AGEDGE, "edgeinfo", sizeof(edgeinfo_t), 1);
-
- int eidx = 0;
- for (n = agfstnode(g); n; n = agnxtnode(g, n)) {
- for (e = agfstout(g, n); e; e = agnxtout(g, e)) {
- ED_id(e) = eidx++;
- }
- }
- if (verbose)
- fprintf(stderr, "setEdgeWeights\n");
- setEdgeWeights(g, verbose);
-
- /* sort edges by non-increasing weight */
- if (verbose)
- fprintf(stderr, "sorting\n");
- edgelist = N_NEW((size_t)(nedges + 1), Agedge_t *); /* NULL at end */
- i = 0;
- for (n = agfstnode(g); n; n = agnxtnode(g, n)) {
- for (e = agfstout(g, n); e; e = agnxtout(g, e)) {
- edgelist[i++] = e;
- }
- }
- qsort(edgelist, nedges, sizeof(Agedge_t *), (qsort_cmpf)cmpe);
-#if 0
- float curwt = -1;
- int cnt = 0;
- for (i = 0; i <= nedges; i++) {
- e = edgelist[i];
- if (e && (ED_wt(e) == curwt))
- cnt++;
- else {
- if (cnt)
- fprintf(stderr, "%f %d\n", curwt, cnt);
- if (e) {
- cnt = 1;
- curwt = ED_wt(e);
- }
- }
- }
-#endif
- if (verbose)
- fprintf(stderr, "heaviest wt %f least wt %f\n", ED_wt(edgelist[0]),
- ED_wt(edgelist[nedges - 1]));
-
- /* compute UMST */
- sg_union = findUMST(g, edgelist, nedges);
- int umst_size = agnedges(sg_union);
- if (verbose)
- fprintf(stderr, " union of maximum spanning trees: %d edges\n",
- umst_size);
-
- /* Find index of the |E|(1-sparse_ratio)th edge */
- index = computeIndex(nedges, sparse_ratio);
- if (verbose)
- fprintf(stderr, " index %lu out of %lu\n", index, nedges);
-
- /* set of edges with weights above threshold */
- /* Add all edges with wt >= wt(edgelist[index]) */
- /* As edgelist is sorted, first index edges */
- int extra_edges = 0;
- for (i = 1; i <= index; i++) {
- e = edgelist[i - 1];
- if (verbose) {
- if (agsubedge(sg_union, e, 0) == NULL)
- extra_edges++;
- }
- agsubedge(sg_union, e, 1);
- }
-
- /* Add any additional edges with same weight as e */
- if (index) {
- threshold = ED_wt(e);
- for (; i <= nedges; i++) {
- e = edgelist[i - 1];
- if (ED_wt(e) >= threshold) {
- if (verbose) {
- if (agsubedge(sg_union, e, 0) == NULL)
- extra_edges++;
- }
- agsubedge(sg_union, e, 1);
- } else
- break;
- }
- }
- if (verbose)
- fprintf(stderr,
- "number of extra edges not in UMST %d total edges %d\n",
- extra_edges, agnedges(sg_union));
-
- /* layout graph sg_union */
- Agsym_t *sym = agattr(g, AGEDGE, "spine", "0");
- int ncnt = 0;
- int ecnt = 0;
- for (n = agfstnode(sg_union); n; n = agnxtnode(sg_union, n)) {
- ncnt++;
- for (e = agfstout(sg_union, n); e; e = agnxtout(sg_union, e)) {
- ecnt++;
- agxset(e, sym, "1");
- }
- }
- if (verbose)
- fprintf(stderr, "final ncnt %d ecnt %d\n", ncnt, ecnt);
-}
-
-#ifdef MAIN
-
-static FILE *openFile(const char *cmd, const char *name)
-{
- FILE *fp;
-
- fp = fopen(name, "w");
- if (!fp) {
- fprintf(stderr, "%s: could not open file %s for writing\n", cmd, name);
- exit(1);
- }
- return fp;
-}
-
-static int setInt(char *s, int *v)
-{
- char *endp;
- long int l = strtol(s, char &endp, 10);
-
- if (s == endp) {
- fprintf(stderr, "Option value \"%s\" must be an integer\n", s);
- return 1;
- }
- if (l < 0) {
- fprintf(stderr, "Option value \"%s\" must be non-negative.\n", s);
- return 1;
- }
- *v = (int)l;
- return 0;
-
-}
-
-static int setFloat(char *s, float *v)
-{
- char *endp;
- float f = strtof(s, &endp);
- if (s == endp) {
- fprintf(stderr, "Option value \"%s\" must be a float\n", s);
- return 1;
- }
- if ((f < 0) || (f > 1)) {
- fprintf(stderr, "Option value \"%s\" must be in the range [0,1]\n",
- s);
- return 1;
- }
- *v = f;
- return 0;
-
-}
-
-static char *Usage = "Usage: %s [-?] [options]\n\
- -r<n> : sparsification ratio [0,1] (0.5) \n\
- -o<outfile> : put output in <outfile> (stderr)\n\
- -v[<val>] : verbose mode \n\
- -? : print usage\n";
-
-static void usage(char *cmd, int v)
-{
- fprintf(v ? stderr : stdout, Usage, cmd);
- exit(v);
-}
-
-static void doOpts(int argc, char *argv[], opts_t * op)
-{
- int c;
- char *cmd = argv[0];
-
- op->outfp = NULL;
- op->Files = NULL;
- op->verbose = 0;
- op->sparse_ratio = 0.5;
-
- opterr = 0;
- while ((c = getopt(argc, argv, "o:r:v::?")) != -1) {
- switch (c) {
- case 'o':
- op->outfp = openFile(cmd, optarg);
- break;
- case 'v':
- if (optarg)
- if (setInt(optarg, &(op->verbose))) {
- fprintf(stderr, "%s: bad value for flag -%c - ignored\n",
- cmd, c);
- }
- }
- else
- op->verbose = 1;
- break;
- case 'r':
- if (setFloat(optarg, &(op->sparse_ratio))) {
- fprintf(stderr, "%s: bad value for flag -%c - ignored\n",
- cmd, c);
- }
- break;
- case '?':
- if (optopt == '\0')
- usage(cmd, 0);
- else {
- fprintf(stderr, "%s: option -%c unrecognized\n",
- cmd, optopt);
- usage(cmd, 1);
- }
- break;
- default:
- break;
- }
- }
- argv += optind;
- argc -= optind;
-
- if (argc)
- op->Files = argv;
- if (op->outfp == NULL)
- op->outfp = stderr;
- if (op->verbose)
- fprintf(stderr, "sparse ratio = %f\n", op->sparse_ratio);
-}
-
-static Agraph_t *gread(FILE * fp)
-{
- return agread(fp, NULL);
-}
-
-int main(int argc, char *argv[])
-{
- opts_t opts;
- ingraph_state ig;
- Agraph_t *g;
-
- doOpts(argc, argv, &opts);
- newIngraph(&ig, opts.Files, gread);
- while ((g = nextGraph(&ig)) != 0) {
- genSpine(g, opts.sparse_ratio, opts.verbose);
- agwrite(g, opts.outfp);
- agclose(g);
- }
-
- return 0;
-}
-#endif
+++ /dev/null
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-<Project DefaultTargets="Build" ToolsVersion="14.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
- <ItemGroup Label="ProjectConfigurations">
- <ProjectConfiguration Include="Debug|Win32">
- <Configuration>Debug</Configuration>
- <Platform>Win32</Platform>
- </ProjectConfiguration>
- <ProjectConfiguration Include="Release|Win32">
- <Configuration>Release</Configuration>
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- </ProjectConfiguration>
- <ProjectConfiguration Include="Debug|x64">
- <Configuration>Debug</Configuration>
- <Platform>x64</Platform>
- </ProjectConfiguration>
- <ProjectConfiguration Include="Release|x64">
- <Configuration>Release</Configuration>
- <Platform>x64</Platform>
- </ProjectConfiguration>
- </ItemGroup>
- <ItemGroup>
- <ClCompile Include="quad.c" />
- <ClCompile Include="spine.c" />
- <ClCompile Include="subset.c" />
- <ClCompile Include="union_find.c" />
- </ItemGroup>
- <ItemGroup>
- <ClInclude Include="quad.h" />
- <ClInclude Include="spine.h" />
- <ClInclude Include="spinehdr.h" />
- <ClInclude Include="subset.h" />
- <ClInclude Include="union_find.h" />
- </ItemGroup>
- <PropertyGroup Label="Globals">
- <ProjectGuid>{4DBC1707-9797-4BAD-8989-08AF459F8840}</ProjectGuid>
- <RootNamespace>spine</RootNamespace>
- <WindowsTargetPlatformVersion>10.0</WindowsTargetPlatformVersion>
- </PropertyGroup>
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projects / graphviz / commitdiff