stuff.c

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/*************************************************************************
 * Copyright (c) 2011 AT&T Intellectual Property
 * All rights reserved. This program and the accompanying materials
 * are made available under the terms of the Eclipse Public License v1.0
 * which accompanies this distribution, and is available at
 * https://www.eclipse.org/legal/epl-v10.html
 *
 * Contributors: Details at https://graphviz.org
 *************************************************************************/
 
 
#include "config.h"
#include        <math.h>
#include        <neatogen/neato.h>
#include        <neatogen/stress.h>
#include        <stdatomic.h>
#include        <stdlib.h>
#include        <time.h>
#include        <util/alloc.h>
#ifndef _WIN32
#include        <unistd.h>
#endif
 
static double Epsilon2;
static Agnode_t *choose_node(graph_t *, int);
static void make_spring(graph_t *, Agnode_t *, Agnode_t *, double);
static void move_node(graph_t *, int, Agnode_t *);
 
static double distvec(double *p0, double *p1, double *vec)
{
    int k;
    double dist = 0.0;
 
    for (k = 0; k < Ndim; k++) {
        vec[k] = p0[k] - p1[k];
        dist += vec[k] * vec[k];
    }
    dist = sqrt(dist);
    return dist;
}
 
double **new_array(int m, int n, double ival)
{
    int i, j;
 
    double **rv = gv_calloc(m, sizeof(double*));
    double *mem = gv_calloc(m * n, sizeof(double));
    for (i = 0; i < m; i++) {
        rv[i] = mem;
        mem += n;
        for (j = 0; j < n; j++)
            rv[i][j] = ival;
    }
    return rv;
}
 
void free_array(double **rv)
{
    if (rv) {
        free(rv[0]);
        free(rv);
    }
}
 
 
static double ***new_3array(int m, int n, int p, double ival)
{
    int i, j, k;
 
    double ***rv = gv_calloc(m + 1, sizeof(double**));
    for (i = 0; i < m; i++) {
        rv[i] = gv_calloc(n + 1, sizeof(double*));
        for (j = 0; j < n; j++) {
            rv[i][j] = gv_calloc(p, sizeof(double));
            for (k = 0; k < p; k++)
                rv[i][j][k] = ival;
        }
        rv[i][j] = NULL;        /* NULL terminate so we can clean up */
    }
    rv[i] = NULL;
    return rv;
}
 
static void free_3array(double ***rv)
{
    int i, j;
 
    if (rv) {
        for (i = 0; rv[i]; i++) {
            for (j = 0; rv[i][j]; j++)
                free(rv[i][j]);
            free(rv[i]);
        }
        free(rv);
    }
}
 
 
/* lenattr:
 * Return 1 if attribute not defined
 * Return 2 if attribute string bad
 */
static int lenattr(edge_t* e, Agsym_t* index, double* val)
{
    char* s;
 
    if (index == NULL)
        return 1;
 
    s = agxget(e, index);
    if (*s == '\0') return 1;
 
    if (sscanf(s, "%lf", val) < 1 || *val < 0 || (*val == 0 && !Nop)) {
        agwarningf("bad edge len \"%s\"", s);
        return 2;
    }
    else
        return 0;
}
 
 
/* degreeKind;
 * Returns degree of n ignoring loops and multiedges.
 * Returns 0, 1 or many (2)
 * For case of 1, returns other endpoint of edge.
 */
static int degreeKind(graph_t * g, node_t * n, node_t ** op)
{
    edge_t *ep;
    int deg = 0;
    node_t *other = NULL;
 
    for (ep = agfstedge(g, n); ep; ep = agnxtedge(g, ep, n)) {
        if (aghead(ep) == agtail(ep))
            continue;           /* ignore loops */
        if (deg == 1) {
            if ((agtail(ep) == n && aghead(ep) == other) ||     /* ignore multiedge */
                (agtail(ep) == other && aghead(ep) == n))
                continue;
            return 2;
        } else {                /* deg == 0 */
            if (agtail(ep) == n)
                other = aghead(ep);
            else
                other = agtail(ep);
            *op = other;
            deg++;
        }
    }
    return deg;
}
 
 
/* prune:
 * np is at end of a chain. If its degree is 0, remove it.
 * If its degree is 1, remove it and recurse.
 * If its degree > 1, stop.
 * The node next is the next node to be visited during iteration.
 * If it is equal to a node being deleted, set it to next one.
 * Delete from root graph, since G may be a connected component subgraph.
 * Return next.
 */
static node_t *prune(graph_t * G, node_t * np, node_t * next)
{
    node_t *other;
    int deg;
 
    while (np) {
        deg = degreeKind(G, np, &other);
        if (deg == 0) {
            if (next == np)
                next = agnxtnode(G, np);
            agdelete(G->root, np);
            np = 0;
        } else if (deg == 1) {
            if (next == np)
                next = agnxtnode(G, np);
            agdelete(G->root, np);
            np = other;
        } else
            np = 0;
 
    }
    return next;
}
 
static double setEdgeLen(graph_t * G, node_t * np, Agsym_t* lenx, double dfltlen)
{
    edge_t *ep;
    double total_len = 0.0;
    double len;
    int err;
 
    for (ep = agfstout(G, np); ep; ep = agnxtout(G, ep)) {
        if ((err = lenattr(ep, lenx, &len))) {
            if (err == 2) agerr(AGPREV, " in %s - setting to %.02f\n", agnameof(G), dfltlen);
            len = dfltlen;
        }
        ED_dist(ep) = len;
        total_len += len;
    }
    return total_len;
}
 
/* scan_graph_mode:
 * Prepare the graph and data structures depending on the layout mode.
 * If Reduce is true, eliminate singletons and trees. Since G may be a
 * subgraph, we remove the nodes from the root graph.
 * Return the number of nodes in the reduced graph.
 */
int scan_graph_mode(graph_t * G, int mode)
{
    int i, nV, nE, deg;
    char *str;
    node_t *np, *xp, *other;
    double total_len = 0.0;
    double dfltlen = 1.0;
    Agsym_t* lenx;
 
    if (Verbose)
        fprintf(stderr, "Scanning graph %s, %d nodes\n", agnameof(G),
                agnnodes(G));
 
 
    /* Eliminate singletons and trees */
    if (Reduce) {
        for (np = agfstnode(G); np; np = xp) {
            xp = agnxtnode(G, np);
            deg = degreeKind(G, np, &other);
            if (deg == 0) {     /* singleton node */
                agdelete(G->root, np);
            } else if (deg == 1) {
                agdelete(G->root, np);
                xp = prune(G, other, xp);
            }
        }
    }
 
    nV = agnnodes(G);
    nE = agnedges(G);
 
    lenx = agattr_text(G, AGEDGE, "len", 0);
    if (mode == MODE_KK) {
        Epsilon = .0001 * nV;
        getdouble(G, "epsilon", &Epsilon);
        if ((str = agget(G->root, "Damping")))
            Damping = atof(str);
        else
            Damping = .99;
        GD_neato_nlist(G) = gv_calloc(nV + 1, sizeof(node_t*));
        for (i = 0, np = agfstnode(G); np; np = agnxtnode(G, np)) {
            GD_neato_nlist(G)[i] = np;
            ND_id(np) = i++;
            ND_heapindex(np) = -1;
            total_len += setEdgeLen(G, np, lenx, dfltlen);
        }
    } else if (mode == MODE_SGD) {
        Epsilon = .01;
        getdouble(G, "epsilon", &Epsilon);
        GD_neato_nlist(G) = gv_calloc(nV + 1, sizeof(node_t *));
        for (i = 0, np = agfstnode(G); np; np = agnxtnode(G, np)) {
            GD_neato_nlist(G)[i] = np;
            ND_id(np) = i++;
            total_len += setEdgeLen(G, np, lenx, dfltlen);
        }
    } else {
        Epsilon = DFLT_TOLERANCE;
        getdouble(G, "epsilon", &Epsilon);
        for (i = 0, np = agfstnode(G); np; np = agnxtnode(G, np)) {
            ND_id(np) = i++;
            total_len += setEdgeLen(G, np, lenx, dfltlen);
        }
    }
 
    str = agget(G, "defaultdist");
    if (str && str[0])
        Initial_dist = fmax(Epsilon, atof(str));
    else
        Initial_dist = total_len / (nE > 0 ? nE : 1) * sqrt(nV) + 1;
 
    if (!Nop && mode == MODE_KK) {
        GD_dist(G) = new_array(nV, nV, Initial_dist);
        GD_spring(G) = new_array(nV, nV, 1.0);
        GD_sum_t(G) = new_array(nV, Ndim, 1.0);
        GD_t(G) = new_3array(nV, nV, Ndim, 0.0);
    }
 
    return nV;
}
 
int scan_graph(graph_t * g)
{
    return scan_graph_mode(g, MODE_KK);
}
 
void free_scan_graph(graph_t * g)
{
    free(GD_neato_nlist(g));
    if (!Nop) {
        free_array(GD_dist(g));
        free_array(GD_spring(g));
        free_array(GD_sum_t(g));
        free_3array(GD_t(g));
        GD_t(g) = NULL;
    }
}
 
void jitter_d(node_t * np, int nG, int n)
{
    int k;
    for (k = n; k < Ndim; k++)
        ND_pos(np)[k] = nG * drand48();
}
 
void jitter3d(node_t * np, int nG)
{
    jitter_d(np, nG, 2);
}
 
void randompos(node_t * np, int nG)
{
    ND_pos(np)[0] = nG * drand48();
    ND_pos(np)[1] = nG * drand48();
    if (Ndim > 2)
        jitter3d(np, nG);
}
 
void initial_positions(graph_t * G, int nG)
{
    int init, i;
    node_t *np;
    static atomic_flag once;
 
    if (Verbose)
        fprintf(stderr, "Setting initial positions\n");
 
    init = checkStart(G, nG, INIT_RANDOM);
    if (init == INIT_REGULAR)
        return;
    if (init == INIT_SELF && !atomic_flag_test_and_set(&once)) {
        agwarningf("start=0 not supported with mode=self - ignored\n");
    }
 
    for (i = 0; (np = GD_neato_nlist(G)[i]); i++) {
        if (hasPos(np))
            continue;
        randompos(np, 1);
    }
}
 
void diffeq_model(graph_t * G, int nG)
{
    int i, j, k;
    double dist, **D, **K, del[MAXDIM], f;
    node_t *vi, *vj;
    edge_t *e;
 
    if (Verbose) {
        fprintf(stderr, "Setting up spring model: ");
        start_timer();
    }
    /* init springs */
    K = GD_spring(G);
    D = GD_dist(G);
    for (i = 0; i < nG; i++) {
        for (j = 0; j < i; j++) {
            f = Spring_coeff / (D[i][j] * D[i][j]);
            if ((e = agfindedge(G, GD_neato_nlist(G)[i], GD_neato_nlist(G)[j])))
                f *= ED_factor(e);
            K[i][j] = K[j][i] = f;
        }
    }
 
    /* init differential equation solver */
    for (i = 0; i < nG; i++)
        for (k = 0; k < Ndim; k++)
            GD_sum_t(G)[i][k] = 0.0;
 
    for (i = 0; (vi = GD_neato_nlist(G)[i]); i++) {
        for (j = 0; j < nG; j++) {
            if (i == j)
                continue;
            vj = GD_neato_nlist(G)[j];
            dist = distvec(ND_pos(vi), ND_pos(vj), del);
            for (k = 0; k < Ndim; k++) {
                GD_t(G)[i][j][k] =
                    GD_spring(G)[i][j] * (del[k] -
                                          GD_dist(G)[i][j] * del[k] /
                                          dist);
                GD_sum_t(G)[i][k] += GD_t(G)[i][j][k];
            }
        }
    }
    if (Verbose) {
        fprintf(stderr, "%.2f sec\n", elapsed_sec());
    }
}
 
/* total_e:
 * Return 2*energy of system.
 */
static double total_e(graph_t * G, int nG)
{
    int i, j, d;
    double e = 0.0;             /* 2*energy */
    double t0;                  /* distance squared */
    double t1;
    node_t *ip, *jp;
 
    for (i = 0; i < nG - 1; i++) {
        ip = GD_neato_nlist(G)[i];
        for (j = i + 1; j < nG; j++) {
            jp = GD_neato_nlist(G)[j];
            for (t0 = 0.0, d = 0; d < Ndim; d++) {
                t1 = ND_pos(ip)[d] - ND_pos(jp)[d];
                t0 += t1 * t1;
            }
            e = e + GD_spring(G)[i][j] *
                (t0 + GD_dist(G)[i][j] * GD_dist(G)[i][j]
                 - 2.0 * GD_dist(G)[i][j] * sqrt(t0));
        }
    }
    return e;
}
 
void solve_model(graph_t * G, int nG)
{
    node_t *np;
 
    Epsilon2 = Epsilon * Epsilon;
 
    while ((np = choose_node(G, nG))) {
        move_node(G, nG, np);
    }
    if (Verbose) {
        fprintf(stderr, "\nfinal e = %f", total_e(G, nG));
        fprintf(stderr, " %d%s iterations %.2f sec\n",
                GD_move(G), GD_move(G) == MaxIter ? "!" : "",
                elapsed_sec());
    }
    if (GD_move(G) == MaxIter)
        agwarningf("Max. iterations (%d) reached on graph %s\n",
              MaxIter, agnameof(G));
}
 
static void update_arrays(graph_t * G, int nG, int i)
{
    int j, k;
    double del[MAXDIM], dist;
    node_t *vi, *vj;
 
    vi = GD_neato_nlist(G)[i];
    for (k = 0; k < Ndim; k++)
        GD_sum_t(G)[i][k] = 0.0;
    for (j = 0; j < nG; j++) {
        if (i == j)
            continue;
        vj = GD_neato_nlist(G)[j];
        dist = distvec(ND_pos(vi), ND_pos(vj), del);
        for (k = 0; k < Ndim; k++) {
            GD_t(G)[i][j][k] =
                GD_spring(G)[i][j] * (del[k] -
                                      GD_dist(G)[i][j] * del[k] / dist);
            GD_sum_t(G)[i][k] += GD_t(G)[i][j][k];
            const double old = GD_t(G)[j][i][k];
            GD_t(G)[j][i][k] = -GD_t(G)[i][j][k];
            GD_sum_t(G)[j][k] += GD_t(G)[j][i][k] - old;
        }
    }
}
 
#define Msub(i,j)  M[(i)*Ndim+(j)]
static void D2E(graph_t * G, int nG, int n, double *M)
{
    int i, l, k;
    node_t *vi, *vn;
    double scale, sq, t[MAXDIM];
    double **K = GD_spring(G);
    double **D = GD_dist(G);
 
    vn = GD_neato_nlist(G)[n];
    for (l = 0; l < Ndim; l++)
        for (k = 0; k < Ndim; k++)
            Msub(l, k) = 0.0;
    for (i = 0; i < nG; i++) {
        if (n == i)
            continue;
        vi = GD_neato_nlist(G)[i];
        sq = 0.0;
        for (k = 0; k < Ndim; k++) {
            t[k] = ND_pos(vn)[k] - ND_pos(vi)[k];
            sq += t[k] * t[k];
        }
        scale = 1 / pow(sq, 1.5);
        for (k = 0; k < Ndim; k++) {
            for (l = 0; l < k; l++)
                Msub(l, k) += K[n][i] * D[n][i] * t[k] * t[l] * scale;
            Msub(k, k) +=
                K[n][i] * (1.0 - D[n][i] * (sq - t[k] * t[k]) * scale);
        }
    }
    for (k = 1; k < Ndim; k++)
        for (l = 0; l < k; l++)
            Msub(k, l) = Msub(l, k);
}
 
node_t *choose_node(graph_t * G, int nG)
{
    int i, k;
    double m, max;
    node_t *choice, *np;
    static int cnt = 0;
 
    cnt++;
    if (GD_move(G) >= MaxIter)
        return NULL;
    max = 0.0;
    choice = NULL;
    for (i = 0; i < nG; i++) {
        np = GD_neato_nlist(G)[i];
        if (ND_pinned(np) > P_SET)
            continue;
        for (m = 0.0, k = 0; k < Ndim; k++)
            m += GD_sum_t(G)[i][k] * GD_sum_t(G)[i][k];
        /* could set the color=energy of the node here */
        if (m > max) {
            choice = np;
            max = m;
        }
    }
    if (max < Epsilon2)
        choice = NULL;
    else {
        if (Verbose && cnt % 100 == 0) {
            fprintf(stderr, "%.3f ", sqrt(max));
            if (cnt % 1000 == 0)
                fprintf(stderr, "\n");
        }
    }
    return choice;
}
 
void move_node(graph_t * G, int nG, node_t * n)
{
    int i, m;
    double b[MAXDIM] = {0};
    double c[MAXDIM] = {0};
 
    m = ND_id(n);
    double *a = gv_calloc((size_t)Ndim * Ndim, sizeof(double));
    D2E(G, nG, m, a);
    for (i = 0; i < Ndim; i++)
        c[i] = -GD_sum_t(G)[m][i];
    solve(a, b, c, Ndim);
    for (i = 0; i < Ndim; i++) {
        b[i] = (Damping + 2 * (1 - Damping) * drand48()) * b[i];
        ND_pos(n)[i] += b[i];
    }
    GD_move(G)++;
    update_arrays(G, nG, m);
    if (test_toggle()) {
        double sum = 0;
        for (i = 0; i < Ndim; i++) {
            sum += fabs(b[i]);
        }                       /* Why not squared? */
        sum = sqrt(sum);
        fprintf(stderr, "%s %.3f\n", agnameof(n), sum);
    }
    free(a);
}
 
static node_t **Heap;
static int Heapsize;
static node_t *Src;
 
static void heapup(node_t * v)
{
    int i, par;
    node_t *u;
 
    for (i = ND_heapindex(v); i > 0; i = par) {
        par = (i - 1) / 2;
        u = Heap[par];
        if (ND_dist(u) <= ND_dist(v))
            break;
        Heap[par] = v;
        ND_heapindex(v) = par;
        Heap[i] = u;
        ND_heapindex(u) = i;
    }
}
 
static void heapdown(node_t * v)
{
    int i, left, right, c;
    node_t *u;
 
    i = ND_heapindex(v);
    while ((left = 2 * i + 1) < Heapsize) {
        right = left + 1;
        if (right < Heapsize && ND_dist(Heap[right]) < ND_dist(Heap[left]))
            c = right;
        else
            c = left;
        u = Heap[c];
        if (ND_dist(v) <= ND_dist(u))
            break;
        Heap[c] = v;
        ND_heapindex(v) = c;
        Heap[i] = u;
        ND_heapindex(u) = i;
        i = c;
    }
}
 
void neato_enqueue(node_t * v)
{
    int i;
 
    assert(ND_heapindex(v) < 0);
    i = Heapsize++;
    ND_heapindex(v) = i;
    Heap[i] = v;
    if (i > 0)
        heapup(v);
}
 
node_t *neato_dequeue(void)
{
    int i;
    node_t *rv, *v;
 
    if (Heapsize == 0)
        return NULL;
    rv = Heap[0];
    i = --Heapsize;
    v = Heap[i];
    Heap[0] = v;
    ND_heapindex(v) = 0;
    if (i > 1)
        heapdown(v);
    ND_heapindex(rv) = -1;
    return rv;
}
 
void shortest_path(graph_t * G, int nG)
{
    node_t *v;
 
    Heap = gv_calloc(nG + 1, sizeof(node_t*));
    if (Verbose) {
        fprintf(stderr, "Calculating shortest paths: ");
        start_timer();
    }
    for (v = agfstnode(G); v; v = agnxtnode(G, v))
        s1(G, v);
    if (Verbose) {
        fprintf(stderr, "%.2f sec\n", elapsed_sec());
    }
    free(Heap);
}
 
void s1(graph_t * G, node_t * node)
{
    node_t *v, *u;
    edge_t *e;
    int t;
    double f;
 
    for (t = 0; (v = GD_neato_nlist(G)[t]); t++)
        ND_dist(v) = Initial_dist;
    Src = node;
    ND_dist(Src) = 0;
    ND_hops(Src) = 0;
    neato_enqueue(Src);
 
    while ((v = neato_dequeue())) {
        if (v != Src)
            make_spring(G, Src, v, ND_dist(v));
        for (e = agfstedge(G, v); e; e = agnxtedge(G, e, v)) {
            if ((u = agtail(e)) == v)
                u = aghead(e);
            f = ND_dist(v) + ED_dist(e);
            if (ND_dist(u) > f) {
                ND_dist(u) = f;
                if (ND_heapindex(u) >= 0)
                    heapup(u);
                else {
                    ND_hops(u) = ND_hops(v) + 1;
                    neato_enqueue(u);
                }
            }
        }
    }
}
 
void make_spring(graph_t * G, node_t * u, node_t * v, double f)
{
    int i, j;
 
    i = ND_id(u);
    j = ND_id(v);
    GD_dist(G)[i][j] = GD_dist(G)[j][i] = f;
}